Starting phenix.real_space_refine on Sat Sep 12 06:43:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6lxd_30005/09_2026/6lxd_30005.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lxd_30005/09_2026/6lxd_30005.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6lxd_30005/09_2026/6lxd_30005.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lxd_30005/09_2026/6lxd_30005.map" model { file = "/net/cci-nas-00/data/ceres_data/6lxd_30005/09_2026/6lxd_30005.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lxd_30005/09_2026/6lxd_30005.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6lxd_30005/09_2026/6lxd_30005.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6lxd_30005/09_2026/6lxd_30005.cif" } resolution = 3.9 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5612 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 72 5.49 5 S 52 5.16 5 C 5705 2.51 5 N 1680 2.21 5 O 1924 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9435 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 918, 7517 Classifications: {'peptide': 918} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 52, 'TRANS': 865} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 205 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "C" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 179 Classifications: {'peptide': 21} Link IDs: {'TRANS': 20} Chain: "D" Number of atoms: 1532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1532 Classifications: {'RNAv2': 72} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 36, 'rna3p_pyr': 32} Link IDs: {'rna2p': 4, 'rna3p': 67} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 928 SG CYS A 561 41.256 73.628 107.458 1.00125.53 S ATOM 1886 SG CYS A 676 43.580 71.223 104.928 1.00125.53 S ATOM 736 SG CYS A 536 57.186 54.545 88.837 1.00135.03 S ATOM 751 SG CYS A 538 58.211 55.298 85.576 1.00158.87 S Time building chain proxies: 1.72, per 1000 atoms: 0.18 Number of scatterers: 9435 At special positions: 0 Unit cell: (76.95, 101.25, 145.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 52 16.00 P 72 15.00 O 1924 8.00 N 1680 7.00 C 5705 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: 0.67 Conformation dependent library (CDL) restraints added in 287.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1401 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 676 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 561 " pdb="ZN ZN A1401 " - pdb=" NE2 HIS A 609 " pdb="ZN ZN A1401 " - pdb=" NE2 HIS A 680 " pdb=" ZN A1402 " pdb="ZN ZN A1402 " - pdb=" NE2 HIS A1026 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 536 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 538 " pdb="ZN ZN A1402 " - pdb=" NE2 HIS A 549 " Number of angles added : 4 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1836 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 6 sheets defined 51.3% alpha, 8.1% beta 26 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 439 through 456 removed outlier: 3.944A pdb=" N GLY A 453 " --> pdb=" O GLU A 449 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLN A 456 " --> pdb=" O LEU A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 459 No H-bonds generated for 'chain 'A' and resid 457 through 459' Processing helix chain 'A' and resid 506 through 511 Processing helix chain 'A' and resid 512 through 514 No H-bonds generated for 'chain 'A' and resid 512 through 514' Processing helix chain 'A' and resid 541 through 545 Processing helix chain 'A' and resid 546 through 550 Processing helix chain 'A' and resid 641 through 653 removed outlier: 3.674A pdb=" N LEU A 645 " --> pdb=" O CYS A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 710 Processing helix chain 'A' and resid 716 through 726 removed outlier: 4.485A pdb=" N ALA A 720 " --> pdb=" O GLU A 716 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASN A 721 " --> pdb=" O GLU A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 737 Processing helix chain 'A' and resid 790 through 803 Processing helix chain 'A' and resid 813 through 829 Processing helix chain 'A' and resid 856 through 883 Proline residue: A 864 - end of helix Processing helix chain 'A' and resid 889 through 897 Processing helix chain 'A' and resid 909 through 920 Processing helix chain 'A' and resid 930 through 935 Processing helix chain 'A' and resid 940 through 951 removed outlier: 4.175A pdb=" N THR A 944 " --> pdb=" O LYS A 940 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 945 " --> pdb=" O GLY A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 987 Processing helix chain 'A' and resid 992 through 1005 removed outlier: 3.682A pdb=" N LEU A 996 " --> pdb=" O GLU A 992 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN A1005 " --> pdb=" O THR A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1015 removed outlier: 4.071A pdb=" N LYS A1015 " --> pdb=" O MET A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1055 Processing helix chain 'A' and resid 1056 through 1069 Processing helix chain 'A' and resid 1074 through 1079 Processing helix chain 'A' and resid 1084 through 1089 Processing helix chain 'A' and resid 1103 through 1115 removed outlier: 3.754A pdb=" N LEU A1107 " --> pdb=" O VAL A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1129 removed outlier: 4.177A pdb=" N LEU A1124 " --> pdb=" O HIS A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1166 Processing helix chain 'A' and resid 1171 through 1180 removed outlier: 4.285A pdb=" N LEU A1177 " --> pdb=" O HIS A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1183 through 1195 Processing helix chain 'A' and resid 1196 through 1200 Processing helix chain 'A' and resid 1213 through 1232 Processing helix chain 'A' and resid 1233 through 1253 removed outlier: 4.045A pdb=" N VAL A1237 " --> pdb=" O ASP A1233 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N PHE A1246 " --> pdb=" O ASN A1242 " (cutoff:3.500A) Proline residue: A1247 - end of helix removed outlier: 4.194A pdb=" N LYS A1250 " --> pdb=" O PHE A1246 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLU A1251 " --> pdb=" O PRO A1247 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1271 removed outlier: 4.235A pdb=" N LEU A1265 " --> pdb=" O PRO A1261 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN A1266 " --> pdb=" O LYS A1262 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1331 Processing helix chain 'A' and resid 1336 through 1348 Processing helix chain 'A' and resid 1350 through 1356 Processing helix chain 'A' and resid 1356 through 1361 Processing helix chain 'A' and resid 1362 through 1364 No H-bonds generated for 'chain 'A' and resid 1362 through 1364' Processing helix chain 'B' and resid 728 through 750 Processing helix chain 'C' and resid 730 through 749 removed outlier: 3.852A pdb=" N LYS C 734 " --> pdb=" O HIS C 730 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLU C 748 " --> pdb=" O GLU C 744 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR C 749 " --> pdb=" O GLU C 745 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 422 through 423 Processing sheet with id=AA2, first strand: chain 'A' and resid 591 through 593 removed outlier: 11.753A pdb=" N GLU A 602 " --> pdb=" O VAL A 578 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N VAL A 578 " --> pdb=" O GLU A 602 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N PHE A 604 " --> pdb=" O ILE A 576 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N CYS A 618 " --> pdb=" O ILE A 629 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 591 through 593 removed outlier: 6.326A pdb=" N PHE A 601 " --> pdb=" O VAL A 686 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL A 686 " --> pdb=" O PHE A 601 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLY A 603 " --> pdb=" O ARG A 684 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 751 through 753 removed outlier: 3.642A pdb=" N ILE A 741 " --> pdb=" O ILE A 852 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE A 852 " --> pdb=" O ILE A 741 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N THR A 743 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N THR A 850 " --> pdb=" O THR A 743 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 756 through 757 Processing sheet with id=AA6, first strand: chain 'A' and resid 1283 through 1290 removed outlier: 7.082A pdb=" N THR A1299 " --> pdb=" O LEU A1287 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N THR A1289 " --> pdb=" O THR A1297 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N THR A1297 " --> pdb=" O THR A1289 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TYR A1298 " --> pdb=" O LYS A1313 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYS A1313 " --> pdb=" O TYR A1298 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL A1300 " --> pdb=" O CYS A1311 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N CYS A1311 " --> pdb=" O VAL A1300 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL A1302 " --> pdb=" O ILE A1309 " (cutoff:3.500A) 346 hydrogen bonds defined for protein. 1005 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 63 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 1.70 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2798 1.34 - 1.46: 1984 1.46 - 1.58: 4797 1.58 - 1.70: 142 1.70 - 1.82: 84 Bond restraints: 9805 Sorted by residual: bond pdb=" N CYS A 561 " pdb=" CA CYS A 561 " ideal model delta sigma weight residual 1.453 1.476 -0.023 1.27e-02 6.20e+03 3.25e+00 bond pdb=" CA ARG A 836 " pdb=" C ARG A 836 " ideal model delta sigma weight residual 1.532 1.521 0.012 9.60e-03 1.09e+04 1.48e+00 bond pdb=" C ASP A 855 " pdb=" N VAL A 856 " ideal model delta sigma weight residual 1.332 1.316 0.016 1.36e-02 5.41e+03 1.42e+00 bond pdb=" C VAL A 714 " pdb=" N PRO A 715 " ideal model delta sigma weight residual 1.334 1.360 -0.027 2.34e-02 1.83e+03 1.29e+00 bond pdb=" N VAL A 856 " pdb=" CA VAL A 856 " ideal model delta sigma weight residual 1.459 1.472 -0.013 1.25e-02 6.40e+03 1.09e+00 ... (remaining 9800 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 12894 1.24 - 2.47: 435 2.47 - 3.71: 223 3.71 - 4.94: 24 4.94 - 6.18: 16 Bond angle restraints: 13592 Sorted by residual: angle pdb=" O VAL A 856 " pdb=" C VAL A 856 " pdb=" N CYS A 857 " ideal model delta sigma weight residual 122.57 126.02 -3.45 1.25e+00 6.40e-01 7.60e+00 angle pdb=" N VAL A 856 " pdb=" CA VAL A 856 " pdb=" C VAL A 856 " ideal model delta sigma weight residual 109.34 103.65 5.69 2.08e+00 2.31e-01 7.48e+00 angle pdb=" N GLU A 823 " pdb=" CA GLU A 823 " pdb=" C GLU A 823 " ideal model delta sigma weight residual 111.07 108.20 2.87 1.07e+00 8.73e-01 7.17e+00 angle pdb=" CA CYS A 561 " pdb=" C CYS A 561 " pdb=" O CYS A 561 " ideal model delta sigma weight residual 121.88 119.06 2.82 1.13e+00 7.83e-01 6.22e+00 angle pdb=" N LEU A 863 " pdb=" CA LEU A 863 " pdb=" C LEU A 863 " ideal model delta sigma weight residual 109.81 115.22 -5.41 2.21e+00 2.05e-01 5.99e+00 ... (remaining 13587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 5122 17.50 - 35.00: 475 35.00 - 52.50: 141 52.50 - 70.00: 43 70.00 - 87.50: 9 Dihedral angle restraints: 5790 sinusoidal: 2962 harmonic: 2828 Sorted by residual: dihedral pdb=" C4' A D 97 " pdb=" C3' A D 97 " pdb=" C2' A D 97 " pdb=" C1' A D 97 " ideal model delta sinusoidal sigma weight residual 36.35 -36.22 72.57 1 3.10e+00 1.04e-01 7.00e+02 dihedral pdb=" C4' U D 96 " pdb=" C3' U D 96 " pdb=" C2' U D 96 " pdb=" C1' U D 96 " ideal model delta sinusoidal sigma weight residual 36.35 -35.89 72.24 1 3.10e+00 1.04e-01 6.94e+02 dihedral pdb=" C4' C D 98 " pdb=" C3' C D 98 " pdb=" C2' C D 98 " pdb=" C1' C D 98 " ideal model delta sinusoidal sigma weight residual 36.34 -35.80 72.14 1 3.10e+00 1.04e-01 6.93e+02 ... (remaining 5787 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1247 0.055 - 0.109: 183 0.109 - 0.164: 15 0.164 - 0.219: 11 0.219 - 0.273: 71 Chirality restraints: 1527 Sorted by residual: chirality pdb=" C2' A D 97 " pdb=" C3' A D 97 " pdb=" O2' A D 97 " pdb=" C1' A D 97 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C2' U D 96 " pdb=" C3' U D 96 " pdb=" O2' U D 96 " pdb=" C1' U D 96 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C2' C D 98 " pdb=" C3' C D 98 " pdb=" O2' C D 98 " pdb=" C1' C D 98 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 1524 not shown) Planarity restraints: 1495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C D 70 " 0.016 2.00e-02 2.50e+03 1.98e-02 8.83e+00 pdb=" N1 C D 70 " -0.013 2.00e-02 2.50e+03 pdb=" C2 C D 70 " 0.043 2.00e-02 2.50e+03 pdb=" O2 C D 70 " -0.032 2.00e-02 2.50e+03 pdb=" N3 C D 70 " -0.002 2.00e-02 2.50e+03 pdb=" C4 C D 70 " 0.006 2.00e-02 2.50e+03 pdb=" N4 C D 70 " 0.003 2.00e-02 2.50e+03 pdb=" C5 C D 70 " -0.008 2.00e-02 2.50e+03 pdb=" C6 C D 70 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A1260 " -0.038 5.00e-02 4.00e+02 5.69e-02 5.17e+00 pdb=" N PRO A1261 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A1261 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A1261 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 580 " -0.035 5.00e-02 4.00e+02 5.26e-02 4.43e+00 pdb=" N PRO A 581 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 581 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 581 " -0.029 5.00e-02 4.00e+02 ... (remaining 1492 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1844 2.77 - 3.30: 9564 3.30 - 3.84: 16679 3.84 - 4.37: 18939 4.37 - 4.90: 29604 Nonbonded interactions: 76630 Sorted by model distance: nonbonded pdb=" O2' G D 35 " pdb=" O4' U D 36 " model vdw 2.239 3.040 nonbonded pdb=" O ILE A 772 " pdb=" OG SER A 844 " model vdw 2.242 3.040 nonbonded pdb=" OH TYR A1024 " pdb=" O LEU A1030 " model vdw 2.246 3.040 nonbonded pdb=" O ARG A1126 " pdb=" OG1 THR A1129 " model vdw 2.272 3.040 nonbonded pdb=" O LYS A 559 " pdb=" NH2 ARG A 570 " model vdw 2.281 3.120 ... (remaining 76625 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 729 through 749) selection = chain 'C' } 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: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.830 Find NCS groups from input model: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 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 : 0.014 0.758 9813 Z= 0.328 Angle : 0.745 29.963 13596 Z= 0.329 Chirality : 0.065 0.273 1527 Planarity : 0.004 0.057 1495 Dihedral : 14.997 87.502 3954 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 0.70 % Allowed : 5.56 % Favored : 93.74 % 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 are not related in a simple way. whole: -3.27 (0.25), residues: 955 helix: -0.89 (0.22), residues: 440 sheet: -2.70 (0.53), residues: 76 loop : -3.51 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1248 TYR 0.009 0.001 TYR A 784 PHE 0.013 0.001 PHE A1252 TRP 0.008 0.001 TRP A1258 HIS 0.003 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.13 ( 9805) covalent geometry : angle 0.63860 / 0.32 (13592) hydrogen bonds : bond 0.12012 / 8.07 ( 407) hydrogen bonds : angle 5.14718 / 3.49 ( 1111) metal coordination : bond 0.47361 / 20.17 ( 8) metal coordination : angle 22.39442 / 11.12 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 162 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 618 CYS cc_start: 0.7720 (t) cc_final: 0.7361 (t) REVERT: A 856 VAL cc_start: 0.8793 (OUTLIER) cc_final: 0.8572 (m) REVERT: A 889 ASP cc_start: 0.8569 (t0) cc_final: 0.8198 (t0) REVERT: A 933 HIS cc_start: 0.7146 (m90) cc_final: 0.6768 (m90) REVERT: A 1059 GLU cc_start: 0.8749 (mp0) cc_final: 0.8455 (mp0) REVERT: A 1111 GLU cc_start: 0.8121 (tt0) cc_final: 0.7891 (tt0) REVERT: A 1235 GLU cc_start: 0.8301 (mp0) cc_final: 0.7970 (mp0) REVERT: A 1326 MET cc_start: 0.8582 (ttm) cc_final: 0.7526 (ttp) REVERT: A 1355 MET cc_start: 0.8495 (mtt) cc_final: 0.8234 (mpp) REVERT: A 1357 TRP cc_start: 0.6978 (t-100) cc_final: 0.6716 (t-100) REVERT: B 735 LEU cc_start: 0.9241 (mt) cc_final: 0.8882 (mt) REVERT: B 742 LEU cc_start: 0.9570 (mm) cc_final: 0.8827 (mm) REVERT: B 744 GLU cc_start: 0.8552 (pp20) cc_final: 0.7952 (pp20) REVERT: B 748 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7854 (mm-30) REVERT: C 735 LEU cc_start: 0.9306 (pp) cc_final: 0.8998 (pp) REVERT: C 736 GLN cc_start: 0.9240 (tp40) cc_final: 0.8623 (tp40) REVERT: C 742 LEU cc_start: 0.9163 (tt) cc_final: 0.8925 (tp) outliers start: 6 outliers final: 1 residues processed: 168 average time/residue: 0.1055 time to fit residues: 23.7619 Evaluate side-chains 101 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 99 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 856 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.0370 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 38 optimal weight: 0.0370 chunk 61 optimal weight: 0.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 624 ASN A 639 ASN ** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 812 GLN A 826 GLN A 888 GLN ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1087 GLN A1136 ASN A1170 HIS A1184 ASN A1197 GLN ** A1222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1318 GLN C 736 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.065410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.053681 restraints weight = 46402.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.055196 restraints weight = 28125.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.056241 restraints weight = 19654.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.056921 restraints weight = 15115.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.057490 restraints weight = 12573.622| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9813 Z= 0.143 Angle : 0.787 14.219 13596 Z= 0.353 Chirality : 0.051 0.445 1527 Planarity : 0.005 0.056 1495 Dihedral : 11.688 122.345 1920 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 1.85 % Allowed : 12.51 % Favored : 85.63 % 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 are not related in a simple way. whole: -2.22 (0.27), residues: 955 helix: 0.17 (0.24), residues: 451 sheet: -2.66 (0.58), residues: 72 loop : -3.18 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 687 TYR 0.012 0.001 TYR A 733 PHE 0.030 0.002 PHE A 762 TRP 0.006 0.001 TRP A1258 HIS 0.009 0.001 HIS A1026 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 9805) covalent geometry : angle 0.77899 / 0.35 (13592) hydrogen bonds : bond 0.04106 / 2.80 ( 407) hydrogen bonds : angle 4.41486 / 2.98 ( 1111) metal coordination : bond 0.03396 / 1.41 ( 8) metal coordination : angle 6.77635 / 3.69 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 823 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8530 (mt-10) REVERT: A 1111 GLU cc_start: 0.7659 (tt0) cc_final: 0.7117 (tm-30) REVERT: A 1154 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7683 (ttp) REVERT: A 1196 MET cc_start: 0.7718 (ptp) cc_final: 0.7479 (mtt) REVERT: A 1355 MET cc_start: 0.8329 (mtt) cc_final: 0.7840 (mmm) REVERT: B 735 LEU cc_start: 0.9052 (mt) cc_final: 0.8423 (mt) REVERT: B 744 GLU cc_start: 0.8468 (pp20) cc_final: 0.7918 (pp20) REVERT: B 748 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7821 (mm-30) REVERT: C 735 LEU cc_start: 0.9220 (pp) cc_final: 0.8974 (pp) outliers start: 16 outliers final: 10 residues processed: 127 average time/residue: 0.0997 time to fit residues: 17.2751 Evaluate side-chains 104 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 823 GLU Chi-restraints excluded: chain A residue 891 CYS Chi-restraints excluded: chain A residue 1036 LEU Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain A residue 1154 MET Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain C residue 730 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 85 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 14 optimal weight: 0.0050 chunk 43 optimal weight: 5.9990 overall best weight: 3.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN ** A 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 ASN ** A1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.059944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.048357 restraints weight = 49795.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.049711 restraints weight = 30574.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.050666 restraints weight = 21719.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.051209 restraints weight = 17032.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.051706 restraints weight = 14580.572| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 9813 Z= 0.248 Angle : 0.846 10.315 13596 Z= 0.391 Chirality : 0.052 0.366 1527 Planarity : 0.005 0.060 1495 Dihedral : 11.882 134.723 1918 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 3.36 % Allowed : 15.30 % Favored : 81.34 % 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 are not related in a simple way. whole: -2.36 (0.26), residues: 955 helix: -0.10 (0.24), residues: 465 sheet: -2.40 (0.54), residues: 78 loop : -3.21 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 967 TYR 0.016 0.002 TYR A1081 PHE 0.041 0.002 PHE A1252 TRP 0.026 0.002 TRP A 725 HIS 0.007 0.002 HIS A1026 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.25 ( 9805) covalent geometry : angle 0.83532 / 0.39 (13592) hydrogen bonds : bond 0.05631 / 3.95 ( 407) hydrogen bonds : angle 4.76552 / 3.20 ( 1111) metal coordination : bond 0.03230 / 1.31 ( 8) metal coordination : angle 7.67600 / 4.16 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 573 HIS cc_start: 0.8057 (OUTLIER) cc_final: 0.7221 (t-90) REVERT: A 823 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8444 (mt-10) REVERT: A 902 HIS cc_start: 0.6158 (OUTLIER) cc_final: 0.5946 (t-90) REVERT: A 1111 GLU cc_start: 0.8099 (tt0) cc_final: 0.7696 (tt0) REVERT: A 1154 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.7915 (ttp) REVERT: A 1329 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8625 (pp) REVERT: B 734 LYS cc_start: 0.9185 (ptmm) cc_final: 0.8968 (ttpt) REVERT: B 735 LEU cc_start: 0.9090 (mt) cc_final: 0.8669 (mt) REVERT: B 737 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8882 (mm-30) REVERT: B 748 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7907 (mm-30) REVERT: C 740 LYS cc_start: 0.9413 (tptm) cc_final: 0.9113 (ttpp) outliers start: 29 outliers final: 16 residues processed: 118 average time/residue: 0.0929 time to fit residues: 15.0170 Evaluate side-chains 103 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 573 HIS Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 823 GLU Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 891 CYS Chi-restraints excluded: chain A residue 902 HIS Chi-restraints excluded: chain A residue 933 HIS Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain A residue 1036 LEU Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain A residue 1154 MET Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain C residue 730 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 70 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 18 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 456 GLN ** A 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1120 HIS ** A1266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.062922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.050961 restraints weight = 48298.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.052375 restraints weight = 29654.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.053371 restraints weight = 21054.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.053994 restraints weight = 16494.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.054512 restraints weight = 13972.231| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9813 Z= 0.133 Angle : 0.749 10.747 13596 Z= 0.341 Chirality : 0.049 0.341 1527 Planarity : 0.004 0.069 1495 Dihedral : 11.539 132.469 1918 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 3.13 % Allowed : 18.66 % Favored : 78.22 % 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 are not related in a simple way. whole: -1.94 (0.27), residues: 955 helix: 0.29 (0.24), residues: 463 sheet: -2.26 (0.58), residues: 72 loop : -3.03 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 687 TYR 0.012 0.001 TYR A 784 PHE 0.050 0.002 PHE A1252 TRP 0.040 0.002 TRP A 725 HIS 0.006 0.001 HIS A1026 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 9805) covalent geometry : angle 0.74198 / 0.34 (13592) hydrogen bonds : bond 0.04405 / 2.98 ( 407) hydrogen bonds : angle 4.46368 / 2.99 ( 1111) metal coordination : bond 0.02687 / 1.08 ( 8) metal coordination : angle 5.94079 / 3.31 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 564 MET cc_start: 0.7220 (pmm) cc_final: 0.6852 (pmm) REVERT: A 573 HIS cc_start: 0.7765 (OUTLIER) cc_final: 0.6814 (t-90) REVERT: A 823 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8479 (mt-10) REVERT: A 1111 GLU cc_start: 0.7678 (tt0) cc_final: 0.7401 (tt0) REVERT: A 1241 MET cc_start: 0.8566 (mmm) cc_final: 0.8099 (mmm) REVERT: A 1285 LYS cc_start: 0.8727 (mmmt) cc_final: 0.8489 (mmmt) REVERT: A 1329 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8665 (pp) REVERT: B 735 LEU cc_start: 0.8971 (mt) cc_final: 0.8750 (mt) REVERT: B 737 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8535 (mm-30) REVERT: B 740 LYS cc_start: 0.8734 (ptmm) cc_final: 0.8080 (ptpp) REVERT: B 748 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7855 (mm-30) REVERT: C 740 LYS cc_start: 0.9407 (tptm) cc_final: 0.9104 (ttpp) outliers start: 27 outliers final: 15 residues processed: 121 average time/residue: 0.0853 time to fit residues: 14.4548 Evaluate side-chains 104 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 573 HIS Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 823 GLU Chi-restraints excluded: chain A residue 891 CYS Chi-restraints excluded: chain A residue 933 HIS Chi-restraints excluded: chain A residue 1036 LEU Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain A residue 1243 VAL Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain B residue 736 GLN Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain C residue 730 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 94 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 90 optimal weight: 9.9990 chunk 33 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.063773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.052127 restraints weight = 48308.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.053599 restraints weight = 29322.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.054573 restraints weight = 20552.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.055317 restraints weight = 16006.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.055747 restraints weight = 13294.414| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9813 Z= 0.123 Angle : 0.745 11.733 13596 Z= 0.338 Chirality : 0.049 0.322 1527 Planarity : 0.004 0.057 1495 Dihedral : 11.382 132.097 1918 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 3.36 % Allowed : 19.47 % Favored : 77.17 % 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 are not related in a simple way. whole: -1.70 (0.28), residues: 955 helix: 0.44 (0.25), residues: 464 sheet: -2.11 (0.58), residues: 72 loop : -2.85 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 687 TYR 0.011 0.001 TYR A 784 PHE 0.051 0.001 PHE A1252 TRP 0.059 0.002 TRP A 725 HIS 0.005 0.001 HIS A1026 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 9805) covalent geometry : angle 0.73862 / 0.34 (13592) hydrogen bonds : bond 0.04236 / 2.87 ( 407) hydrogen bonds : angle 4.39710 / 2.95 ( 1111) metal coordination : bond 0.02319 / 0.94 ( 8) metal coordination : angle 5.50046 / 3.06 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 722 MET cc_start: 0.7266 (ppp) cc_final: 0.7003 (ppp) REVERT: A 902 HIS cc_start: 0.6142 (OUTLIER) cc_final: 0.5910 (t-90) REVERT: A 977 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7306 (mt-10) REVERT: A 1036 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8107 (mm) REVERT: A 1111 GLU cc_start: 0.7762 (tt0) cc_final: 0.7473 (tt0) REVERT: A 1154 MET cc_start: 0.8128 (ptp) cc_final: 0.7676 (ttp) REVERT: A 1241 MET cc_start: 0.8427 (mmm) cc_final: 0.7830 (mmm) REVERT: A 1260 ASP cc_start: 0.6704 (t70) cc_final: 0.6263 (t70) REVERT: A 1329 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8650 (pp) REVERT: B 737 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8786 (mm-30) REVERT: B 748 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7843 (mm-30) REVERT: C 740 LYS cc_start: 0.9357 (tptm) cc_final: 0.9046 (ttpp) outliers start: 29 outliers final: 18 residues processed: 119 average time/residue: 0.0958 time to fit residues: 16.0662 Evaluate side-chains 105 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 891 CYS Chi-restraints excluded: chain A residue 902 HIS Chi-restraints excluded: chain A residue 933 HIS Chi-restraints excluded: chain A residue 1036 LEU Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1243 VAL Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain C residue 730 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 5.9990 chunk 86 optimal weight: 0.4980 chunk 45 optimal weight: 0.0770 chunk 77 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 19 optimal weight: 0.3980 chunk 78 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.064003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.052212 restraints weight = 47703.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.053667 restraints weight = 28843.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.054618 restraints weight = 20246.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.055360 restraints weight = 15818.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.055813 restraints weight = 13157.645| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9813 Z= 0.122 Angle : 0.749 11.784 13596 Z= 0.338 Chirality : 0.049 0.305 1527 Planarity : 0.004 0.053 1495 Dihedral : 11.289 131.691 1918 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 3.48 % Allowed : 19.81 % Favored : 76.71 % 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 are not related in a simple way. whole: -1.60 (0.28), residues: 955 helix: 0.48 (0.25), residues: 465 sheet: -2.15 (0.57), residues: 72 loop : -2.74 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 746 TYR 0.011 0.001 TYR A 784 PHE 0.041 0.001 PHE A1252 TRP 0.044 0.002 TRP A 725 HIS 0.004 0.001 HIS A1026 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 9805) covalent geometry : angle 0.74396 / 0.34 (13592) hydrogen bonds : bond 0.04178 / 2.84 ( 407) hydrogen bonds : angle 4.38012 / 2.94 ( 1111) metal coordination : bond 0.02155 / 0.88 ( 8) metal coordination : angle 5.31441 / 2.96 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 902 HIS cc_start: 0.6343 (OUTLIER) cc_final: 0.5985 (t-90) REVERT: A 908 MET cc_start: 0.7793 (tmm) cc_final: 0.7488 (tmm) REVERT: A 977 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7261 (mt-10) REVERT: A 1111 GLU cc_start: 0.7741 (tt0) cc_final: 0.7448 (tt0) REVERT: A 1154 MET cc_start: 0.8053 (ptp) cc_final: 0.7557 (ttp) REVERT: A 1225 ILE cc_start: 0.9459 (pt) cc_final: 0.9092 (tt) REVERT: A 1241 MET cc_start: 0.8335 (mmm) cc_final: 0.7771 (mmm) REVERT: A 1329 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8789 (pp) REVERT: A 1355 MET cc_start: 0.8029 (mtt) cc_final: 0.7534 (mmm) REVERT: B 734 LYS cc_start: 0.9263 (ptmm) cc_final: 0.8941 (ptmm) REVERT: B 748 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7864 (mm-30) outliers start: 30 outliers final: 20 residues processed: 117 average time/residue: 0.0960 time to fit residues: 15.9207 Evaluate side-chains 104 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 891 CYS Chi-restraints excluded: chain A residue 902 HIS Chi-restraints excluded: chain A residue 933 HIS Chi-restraints excluded: chain A residue 1036 LEU Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1243 VAL Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain C residue 730 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 13 optimal weight: 4.9990 chunk 38 optimal weight: 0.3980 chunk 75 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 80 optimal weight: 0.0010 chunk 94 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 overall best weight: 2.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 902 HIS ** A1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1259 ASN ** A1266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.060992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.049752 restraints weight = 48786.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.051142 restraints weight = 29340.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.052108 restraints weight = 20607.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.052712 restraints weight = 15985.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.053212 restraints weight = 13459.531| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9813 Z= 0.200 Angle : 0.835 11.757 13596 Z= 0.382 Chirality : 0.052 0.335 1527 Planarity : 0.005 0.049 1495 Dihedral : 11.478 132.128 1918 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 3.71 % Allowed : 19.93 % Favored : 76.36 % 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 are not related in a simple way. whole: -1.73 (0.27), residues: 955 helix: 0.26 (0.25), residues: 466 sheet: -2.03 (0.57), residues: 72 loop : -2.69 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 746 TYR 0.016 0.002 TYR A 733 PHE 0.049 0.002 PHE A1252 TRP 0.059 0.003 TRP A 725 HIS 0.005 0.001 HIS A1026 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.20 ( 9805) covalent geometry : angle 0.82745 / 0.38 (13592) hydrogen bonds : bond 0.05174 / 3.58 ( 407) hydrogen bonds : angle 4.73981 / 3.16 ( 1111) metal coordination : bond 0.02064 / 0.86 ( 8) metal coordination : angle 6.63127 / 3.58 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 85 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 573 HIS cc_start: 0.7786 (OUTLIER) cc_final: 0.7043 (t-90) REVERT: A 682 MET cc_start: 0.7547 (OUTLIER) cc_final: 0.7295 (ppp) REVERT: A 977 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7305 (mt-10) REVERT: A 1005 GLN cc_start: 0.8161 (pt0) cc_final: 0.7932 (pt0) REVERT: A 1036 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8161 (mm) REVERT: A 1111 GLU cc_start: 0.7998 (tt0) cc_final: 0.7596 (tt0) REVERT: A 1154 MET cc_start: 0.8030 (ptp) cc_final: 0.7594 (ttp) REVERT: A 1225 ILE cc_start: 0.9437 (pt) cc_final: 0.9115 (tt) REVERT: A 1241 MET cc_start: 0.8518 (mmm) cc_final: 0.8284 (mmm) REVERT: A 1329 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8753 (pp) REVERT: B 734 LYS cc_start: 0.9254 (ptmm) cc_final: 0.8879 (ttpt) REVERT: B 738 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8606 (mm-30) REVERT: B 748 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7843 (mm-30) REVERT: C 729 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7453 (tt) outliers start: 32 outliers final: 20 residues processed: 109 average time/residue: 0.0881 time to fit residues: 13.7981 Evaluate side-chains 102 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 573 HIS Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 725 TRP Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 891 CYS Chi-restraints excluded: chain A residue 933 HIS Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain A residue 1036 LEU Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1243 VAL Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain B residue 736 GLN Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain C residue 729 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 64 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 39 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 47 optimal weight: 0.2980 chunk 13 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.062771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.051055 restraints weight = 48090.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.052445 restraints weight = 29145.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.053439 restraints weight = 20546.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.054106 restraints weight = 15991.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.054573 restraints weight = 13421.407| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9813 Z= 0.137 Angle : 0.802 12.753 13596 Z= 0.363 Chirality : 0.051 0.313 1527 Planarity : 0.004 0.048 1495 Dihedral : 11.358 131.863 1918 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 3.24 % Allowed : 20.86 % Favored : 75.90 % 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 are not related in a simple way. whole: -1.60 (0.28), residues: 955 helix: 0.41 (0.25), residues: 464 sheet: -2.16 (0.59), residues: 70 loop : -2.63 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 746 TYR 0.013 0.001 TYR A 784 PHE 0.044 0.001 PHE A1252 TRP 0.057 0.002 TRP A 725 HIS 0.005 0.001 HIS A1026 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 ( 9805) covalent geometry : angle 0.79614 / 0.36 (13592) hydrogen bonds : bond 0.04548 / 3.10 ( 407) hydrogen bonds : angle 4.53362 / 3.03 ( 1111) metal coordination : bond 0.02271 / 0.92 ( 8) metal coordination : angle 5.68201 / 3.15 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 573 HIS cc_start: 0.7645 (OUTLIER) cc_final: 0.6873 (t-90) REVERT: A 682 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.7271 (ppp) REVERT: A 977 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7421 (mt-10) REVERT: A 1111 GLU cc_start: 0.7852 (tt0) cc_final: 0.7500 (tt0) REVERT: A 1154 MET cc_start: 0.8087 (ptp) cc_final: 0.7627 (ttp) REVERT: A 1196 MET cc_start: 0.8191 (mtm) cc_final: 0.7982 (mpp) REVERT: A 1225 ILE cc_start: 0.9438 (pt) cc_final: 0.9093 (tt) REVERT: A 1241 MET cc_start: 0.8258 (mmm) cc_final: 0.8015 (mmm) REVERT: A 1329 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8830 (pp) REVERT: B 734 LYS cc_start: 0.9320 (ptmm) cc_final: 0.8943 (ttpt) REVERT: B 738 GLU cc_start: 0.9025 (mm-30) cc_final: 0.8594 (mm-30) REVERT: B 748 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7840 (mm-30) REVERT: C 729 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7536 (tt) outliers start: 28 outliers final: 18 residues processed: 112 average time/residue: 0.0851 time to fit residues: 13.6081 Evaluate side-chains 104 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 573 HIS Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 725 TRP Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 891 CYS Chi-restraints excluded: chain A residue 933 HIS Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1243 VAL Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain B residue 736 GLN Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain C residue 729 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 20 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 10 optimal weight: 0.4980 chunk 8 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.062257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.050910 restraints weight = 48508.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.052299 restraints weight = 29131.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.053296 restraints weight = 20474.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.053969 restraints weight = 15879.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.054461 restraints weight = 13192.953| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9813 Z= 0.160 Angle : 0.840 16.891 13596 Z= 0.379 Chirality : 0.052 0.304 1527 Planarity : 0.004 0.048 1495 Dihedral : 11.373 131.917 1918 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 3.01 % Allowed : 21.32 % Favored : 75.67 % 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 are not related in a simple way. whole: -1.64 (0.28), residues: 955 helix: 0.32 (0.25), residues: 465 sheet: -2.07 (0.59), residues: 70 loop : -2.61 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 746 TYR 0.013 0.001 TYR A 784 PHE 0.025 0.001 PHE A 669 TRP 0.057 0.002 TRP A 725 HIS 0.004 0.001 HIS A1026 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 9805) covalent geometry : angle 0.83400 / 0.38 (13592) hydrogen bonds : bond 0.04688 / 3.18 ( 407) hydrogen bonds : angle 4.59433 / 3.07 ( 1111) metal coordination : bond 0.02112 / 0.86 ( 8) metal coordination : angle 6.07200 / 3.32 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 85 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 573 HIS cc_start: 0.7663 (OUTLIER) cc_final: 0.6894 (t-90) REVERT: A 682 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.7283 (ppp) REVERT: A 722 MET cc_start: 0.7148 (ppp) cc_final: 0.6856 (ppp) REVERT: A 977 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7423 (mt-10) REVERT: A 1005 GLN cc_start: 0.8079 (pt0) cc_final: 0.7873 (pt0) REVERT: A 1111 GLU cc_start: 0.7866 (tt0) cc_final: 0.7508 (tt0) REVERT: A 1154 MET cc_start: 0.8101 (ptp) cc_final: 0.7641 (ttp) REVERT: A 1196 MET cc_start: 0.8218 (mtm) cc_final: 0.7743 (mpp) REVERT: A 1225 ILE cc_start: 0.9438 (pt) cc_final: 0.9107 (tt) REVERT: A 1241 MET cc_start: 0.8308 (mmm) cc_final: 0.8060 (mmm) REVERT: B 734 LYS cc_start: 0.9238 (ptmm) cc_final: 0.8831 (ttpt) REVERT: B 737 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8601 (mm-30) REVERT: B 738 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8542 (mm-30) REVERT: B 748 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7826 (mm-30) REVERT: C 729 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7494 (tt) outliers start: 26 outliers final: 19 residues processed: 106 average time/residue: 0.0905 time to fit residues: 13.6310 Evaluate side-chains 105 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 573 HIS Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 725 TRP Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 891 CYS Chi-restraints excluded: chain A residue 933 HIS Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1243 VAL Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1357 TRP Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain C residue 729 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 88 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.062125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.050800 restraints weight = 48376.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.052236 restraints weight = 29142.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.053222 restraints weight = 20356.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.053860 restraints weight = 15757.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.054350 restraints weight = 13146.321| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9813 Z= 0.164 Angle : 0.857 16.358 13596 Z= 0.387 Chirality : 0.053 0.353 1527 Planarity : 0.004 0.048 1495 Dihedral : 11.376 132.016 1918 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 2.90 % Allowed : 21.67 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.28), residues: 955 helix: 0.32 (0.25), residues: 465 sheet: -1.99 (0.60), residues: 70 loop : -2.60 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 746 TYR 0.013 0.002 TYR A 784 PHE 0.025 0.002 PHE A 669 TRP 0.057 0.002 TRP A 725 HIS 0.004 0.001 HIS A1026 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 ( 9805) covalent geometry : angle 0.85039 / 0.39 (13592) hydrogen bonds : bond 0.04775 / 3.25 ( 407) hydrogen bonds : angle 4.61246 / 3.08 ( 1111) metal coordination : bond 0.02130 / 0.87 ( 8) metal coordination : angle 6.17028 / 3.37 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 573 HIS cc_start: 0.7675 (OUTLIER) cc_final: 0.6917 (t-90) REVERT: A 682 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.7276 (ppp) REVERT: A 722 MET cc_start: 0.7141 (ppp) cc_final: 0.6844 (ppp) REVERT: A 977 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7417 (mt-10) REVERT: A 1005 GLN cc_start: 0.8083 (pt0) cc_final: 0.7873 (pt0) REVERT: A 1111 GLU cc_start: 0.7876 (tt0) cc_final: 0.7525 (tt0) REVERT: A 1154 MET cc_start: 0.8109 (ptp) cc_final: 0.7648 (ttp) REVERT: A 1196 MET cc_start: 0.8218 (mtm) cc_final: 0.7744 (mpp) REVERT: A 1225 ILE cc_start: 0.9430 (pt) cc_final: 0.9102 (tt) REVERT: A 1241 MET cc_start: 0.8249 (mmm) cc_final: 0.8007 (mmm) REVERT: B 734 LYS cc_start: 0.9233 (ptmm) cc_final: 0.8923 (ttpp) REVERT: B 737 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8645 (mm-30) REVERT: B 738 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8558 (mm-30) REVERT: B 748 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7832 (mm-30) REVERT: C 729 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7505 (tt) outliers start: 25 outliers final: 20 residues processed: 103 average time/residue: 0.0884 time to fit residues: 13.1145 Evaluate side-chains 107 residues out of total 865 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 573 HIS Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 725 TRP Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 891 CYS Chi-restraints excluded: chain A residue 933 HIS Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain A residue 1140 LEU Chi-restraints excluded: chain A residue 1148 PHE Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1243 VAL Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1357 TRP Chi-restraints excluded: chain B residue 736 GLN Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain C residue 729 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 45 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 20 optimal weight: 0.0980 chunk 43 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.062677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.051355 restraints weight = 47706.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.052737 restraints weight = 28708.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.053785 restraints weight = 20198.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.054397 restraints weight = 15533.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.054912 restraints weight = 12973.851| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9813 Z= 0.146 Angle : 0.853 14.888 13596 Z= 0.387 Chirality : 0.053 0.330 1527 Planarity : 0.004 0.047 1495 Dihedral : 11.333 131.937 1918 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 2.78 % Allowed : 22.13 % Favored : 75.09 % 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 are not related in a simple way. whole: -1.60 (0.28), residues: 955 helix: 0.35 (0.25), residues: 465 sheet: -1.90 (0.61), residues: 70 loop : -2.60 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 746 TYR 0.013 0.001 TYR A 784 PHE 0.026 0.001 PHE A 669 TRP 0.056 0.002 TRP A 725 HIS 0.005 0.001 HIS A1026 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 ( 9805) covalent geometry : angle 0.84749 / 0.39 (13592) hydrogen bonds : bond 0.04695 / 3.20 ( 407) hydrogen bonds : angle 4.60938 / 3.07 ( 1111) metal coordination : bond 0.02204 / 0.90 ( 8) metal coordination : angle 5.76916 / 3.18 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1363.46 seconds wall clock time: 24 minutes 27.02 seconds (1467.02 seconds total)