Starting phenix.real_space_refine on Thu Sep 26 22:59:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lxd_30005/09_2024/6lxd_30005.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lxd_30005/09_2024/6lxd_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lxd_30005/09_2024/6lxd_30005.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lxd_30005/09_2024/6lxd_30005.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lxd_30005/09_2024/6lxd_30005.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lxd_30005/09_2024/6lxd_30005.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: {'RNA': 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: 6.13, per 1000 atoms: 0.65 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: 2.34 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 3.50 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: 3.97 Time building geometry restraints manager: 2.75 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: 13073 1.24 - 2.47: 402 2.47 - 3.71: 85 3.71 - 4.94: 16 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: 5277 17.50 - 35.00: 474 35.00 - 52.50: 147 52.50 - 70.00: 104 70.00 - 87.50: 20 Dihedral angle restraints: 6022 sinusoidal: 3194 harmonic: 2828 Sorted by residual: dihedral pdb=" CA ARG A 463 " pdb=" C ARG A 463 " pdb=" N PRO A 464 " pdb=" CA PRO A 464 " ideal model delta harmonic sigma weight residual 180.00 160.73 19.27 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA ALA A 780 " pdb=" C ALA A 780 " pdb=" N GLN A 781 " pdb=" CA GLN A 781 " ideal model delta harmonic sigma weight residual 180.00 160.97 19.03 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA PRO A 779 " pdb=" C PRO A 779 " pdb=" N ALA A 780 " pdb=" CA ALA A 780 " ideal model delta harmonic sigma weight residual -180.00 -161.46 -18.54 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 6019 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1321 0.054 - 0.107: 187 0.107 - 0.161: 17 0.161 - 0.215: 1 0.215 - 0.269: 1 Chirality restraints: 1527 Sorted by residual: chirality pdb=" CA VAL A 856 " pdb=" N VAL A 856 " pdb=" C VAL A 856 " pdb=" CB VAL A 856 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA CYS A 561 " pdb=" N CYS A 561 " pdb=" C CYS A 561 " pdb=" CB CYS A 561 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.20e-01 chirality pdb=" CB THR A 438 " pdb=" CA THR A 438 " pdb=" OG1 THR A 438 " pdb=" CG2 THR A 438 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.14e-01 ... (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: 0.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 29.480 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 9805 Z= 0.158 Angle : 0.548 6.175 13592 Z= 0.302 Chirality : 0.037 0.269 1527 Planarity : 0.004 0.057 1495 Dihedral : 16.821 87.502 4186 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.008 0.001 TRP A1258 HIS 0.003 0.001 HIS A 519 PHE 0.013 0.001 PHE A1252 TYR 0.009 0.001 TYR A 784 ARG 0.002 0.000 ARG A1248 *********************** 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 fitting. rotamer outliers: 6 poor density : 162 time to evaluate : 1.132 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: 0.2778 time to fit residues: 61.1170 Evaluate side-chains 101 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 99 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 86 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 609 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 888 GLN A 919 ASN A1062 GLN A1087 GLN A1120 HIS A1136 ASN ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1184 ASN ** A1197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1318 GLN A1350 GLN C 736 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9805 Z= 0.271 Angle : 0.671 7.338 13592 Z= 0.340 Chirality : 0.040 0.147 1527 Planarity : 0.005 0.053 1495 Dihedral : 16.927 74.304 2152 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.32 % Favored : 90.58 % Rotamer: Outliers : 2.32 % Allowed : 13.67 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.26), residues: 955 helix: -0.12 (0.23), residues: 456 sheet: -2.70 (0.56), residues: 72 loop : -3.22 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 412 HIS 0.008 0.001 HIS A1026 PHE 0.027 0.002 PHE A 762 TYR 0.014 0.002 TYR A 733 ARG 0.008 0.001 ARG A 687 *********************** 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 126 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 106 time to evaluate : 0.994 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: A 438 THR cc_start: 0.6636 (OUTLIER) cc_final: 0.3989 (t) REVERT: A 522 LEU cc_start: 0.8061 (mm) cc_final: 0.7431 (pp) REVERT: A 564 MET cc_start: 0.7367 (pmm) cc_final: 0.7122 (pmm) REVERT: A 823 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8503 (mt-10) REVERT: A 917 LEU cc_start: 0.9276 (tp) cc_final: 0.8898 (mt) REVERT: A 1036 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8360 (mm) REVERT: A 1059 GLU cc_start: 0.8682 (mp0) cc_final: 0.8445 (mp0) REVERT: A 1111 GLU cc_start: 0.8020 (tt0) cc_final: 0.7240 (tm-30) REVERT: A 1154 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8093 (ttp) REVERT: A 1235 GLU cc_start: 0.8154 (mp0) cc_final: 0.7827 (mp0) REVERT: A 1350 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.7963 (tm-30) REVERT: A 1355 MET cc_start: 0.8448 (mtt) cc_final: 0.8069 (mmt) REVERT: B 735 LEU cc_start: 0.9086 (mt) cc_final: 0.8875 (mt) REVERT: B 736 GLN cc_start: 0.8933 (pt0) cc_final: 0.8595 (pt0) REVERT: B 737 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8763 (mm-30) REVERT: B 740 LYS cc_start: 0.8641 (ptmm) cc_final: 0.8047 (ptpp) REVERT: B 742 LEU cc_start: 0.9597 (mm) cc_final: 0.9279 (mm) REVERT: B 748 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7861 (mm-30) REVERT: C 735 LEU cc_start: 0.9259 (pp) cc_final: 0.9026 (pp) outliers start: 20 outliers final: 11 residues processed: 122 average time/residue: 0.2544 time to fit residues: 41.8140 Evaluate side-chains 98 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 82 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 THR 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 782 LEU Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 823 GLU Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 891 CYS 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 1154 MET Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1350 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 63 optimal weight: 0.1980 chunk 25 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 82 optimal weight: 0.6980 chunk 31 optimal weight: 20.0000 chunk 74 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN ** 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 791 GLN A1170 HIS A1197 GLN A1256 GLN ** A1266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9805 Z= 0.238 Angle : 0.636 7.733 13592 Z= 0.323 Chirality : 0.040 0.173 1527 Planarity : 0.005 0.060 1495 Dihedral : 16.788 74.081 2151 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 3.24 % Allowed : 15.64 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.27), residues: 955 helix: 0.11 (0.24), residues: 462 sheet: -2.58 (0.56), residues: 72 loop : -3.18 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 725 HIS 0.007 0.001 HIS A1026 PHE 0.045 0.002 PHE A1252 TYR 0.015 0.001 TYR A 733 ARG 0.005 0.001 ARG A 961 *********************** 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 134 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 106 time to evaluate : 0.971 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: A 564 MET cc_start: 0.7427 (pmm) cc_final: 0.7097 (pmm) REVERT: A 573 HIS cc_start: 0.7969 (OUTLIER) cc_final: 0.6870 (t-90) REVERT: A 823 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8505 (mt-10) REVERT: A 917 LEU cc_start: 0.9307 (tp) cc_final: 0.8895 (mt) REVERT: A 1036 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8236 (mm) REVERT: A 1111 GLU cc_start: 0.7789 (tt0) cc_final: 0.7532 (tt0) REVERT: A 1154 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8117 (ttp) REVERT: A 1329 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8645 (pp) REVERT: B 735 LEU cc_start: 0.9164 (mt) cc_final: 0.8954 (mt) REVERT: B 736 GLN cc_start: 0.8964 (pt0) cc_final: 0.8590 (pt0) REVERT: B 737 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8738 (mm-30) REVERT: B 740 LYS cc_start: 0.8653 (ptmm) cc_final: 0.8055 (ptpp) REVERT: B 748 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7928 (mm-30) REVERT: C 740 LYS cc_start: 0.9387 (tptm) cc_final: 0.9063 (ttpp) outliers start: 28 outliers final: 15 residues processed: 128 average time/residue: 0.2367 time to fit residues: 41.5851 Evaluate side-chains 110 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 90 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 810 VAL 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 98 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 82 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 826 GLN A 902 HIS A1256 GLN ** A1266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9805 Z= 0.355 Angle : 0.752 12.570 13592 Z= 0.383 Chirality : 0.044 0.214 1527 Planarity : 0.005 0.058 1495 Dihedral : 16.835 74.202 2151 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.95 % Favored : 89.95 % Rotamer: Outliers : 4.40 % Allowed : 17.15 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.27), residues: 955 helix: -0.15 (0.24), residues: 464 sheet: -2.21 (0.53), residues: 78 loop : -3.01 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 725 HIS 0.006 0.002 HIS A1026 PHE 0.046 0.002 PHE A1252 TYR 0.020 0.002 TYR A1081 ARG 0.005 0.001 ARG A 967 *********************** 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 130 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 92 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 TRP cc_start: 0.8390 (m-90) cc_final: 0.8126 (m-90) REVERT: A 573 HIS cc_start: 0.8262 (OUTLIER) cc_final: 0.7666 (t-90) REVERT: A 823 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8348 (mt-10) REVERT: A 1036 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8271 (mm) REVERT: A 1111 GLU cc_start: 0.8124 (tt0) cc_final: 0.7732 (tt0) REVERT: A 1154 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8278 (ttp) REVERT: A 1235 GLU cc_start: 0.8218 (mp0) cc_final: 0.7971 (mp0) REVERT: A 1329 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8708 (pp) REVERT: A 1355 MET cc_start: 0.8328 (mtt) cc_final: 0.7945 (mmt) REVERT: B 736 GLN cc_start: 0.9036 (pt0) cc_final: 0.8725 (pt0) REVERT: B 737 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8757 (mm-30) REVERT: B 740 LYS cc_start: 0.8561 (ptmm) cc_final: 0.8001 (ptpp) REVERT: B 742 LEU cc_start: 0.9643 (OUTLIER) cc_final: 0.9326 (mm) REVERT: B 748 GLU cc_start: 0.8333 (tm-30) cc_final: 0.7879 (mm-30) REVERT: C 740 LYS cc_start: 0.9473 (tptm) cc_final: 0.9163 (ttpp) outliers start: 38 outliers final: 19 residues processed: 123 average time/residue: 0.2177 time to fit residues: 37.6676 Evaluate side-chains 101 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 76 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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 565 THR Chi-restraints excluded: chain A residue 573 HIS Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 725 TRP 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 933 HIS Chi-restraints excluded: chain A residue 964 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 1138 LEU 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** A1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9805 Z= 0.294 Angle : 0.719 10.808 13592 Z= 0.363 Chirality : 0.043 0.171 1527 Planarity : 0.005 0.051 1495 Dihedral : 16.775 74.096 2151 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 4.06 % Allowed : 19.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.27), residues: 955 helix: 0.03 (0.24), residues: 464 sheet: -2.05 (0.58), residues: 72 loop : -2.86 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 725 HIS 0.006 0.001 HIS A1026 PHE 0.039 0.002 PHE A1252 TYR 0.015 0.002 TYR A1081 ARG 0.005 0.001 ARG A 967 *********************** 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 129 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 94 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 722 MET cc_start: 0.7699 (ppp) cc_final: 0.7231 (ppp) REVERT: A 823 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8349 (mt-10) REVERT: A 1036 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8159 (mm) REVERT: A 1154 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8252 (ttp) REVERT: A 1235 GLU cc_start: 0.8128 (mp0) cc_final: 0.7879 (mp0) REVERT: A 1241 MET cc_start: 0.8754 (mmm) cc_final: 0.8326 (mmm) REVERT: A 1260 ASP cc_start: 0.7542 (t70) cc_final: 0.6934 (t70) REVERT: A 1329 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8783 (pp) REVERT: B 734 LYS cc_start: 0.9211 (ptmt) cc_final: 0.8956 (ptmm) REVERT: B 742 LEU cc_start: 0.9617 (OUTLIER) cc_final: 0.9339 (mm) REVERT: B 748 GLU cc_start: 0.8357 (tm-30) cc_final: 0.7884 (mm-30) REVERT: C 740 LYS cc_start: 0.9437 (tptm) cc_final: 0.9112 (ttpp) outliers start: 35 outliers final: 23 residues processed: 120 average time/residue: 0.2374 time to fit residues: 40.2365 Evaluate side-chains 105 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 77 time to evaluate : 1.095 ------------------------------------------------------------------------------- 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 565 THR Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 725 TRP Chi-restraints excluded: chain A residue 787 ASP Chi-restraints excluded: chain A residue 823 GLU Chi-restraints excluded: chain A residue 825 LEU 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 920 CYS Chi-restraints excluded: chain A residue 933 HIS Chi-restraints excluded: chain A residue 964 HIS Chi-restraints excluded: chain A residue 1036 LEU 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 1154 MET 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 746 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 4.9990 chunk 24 optimal weight: 0.4980 chunk 98 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 HIS ** 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** ** A1087 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9805 Z= 0.248 Angle : 0.696 13.043 13592 Z= 0.348 Chirality : 0.042 0.163 1527 Planarity : 0.005 0.050 1495 Dihedral : 16.649 74.057 2151 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 3.94 % Allowed : 20.86 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.27), residues: 955 helix: 0.12 (0.24), residues: 465 sheet: -2.00 (0.57), residues: 72 loop : -2.84 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 725 HIS 0.006 0.001 HIS A1026 PHE 0.043 0.002 PHE A1252 TYR 0.017 0.002 TYR A1236 ARG 0.005 0.001 ARG C 746 *********************** 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 123 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 89 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 MET cc_start: 0.8332 (tmm) cc_final: 0.7993 (tmm) REVERT: A 573 HIS cc_start: 0.8096 (OUTLIER) cc_final: 0.7189 (t-90) REVERT: A 722 MET cc_start: 0.7685 (ppp) cc_final: 0.7436 (ppp) REVERT: A 823 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8344 (mt-10) REVERT: A 1005 GLN cc_start: 0.8113 (pt0) cc_final: 0.7867 (pt0) REVERT: A 1036 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8154 (mm) REVERT: A 1111 GLU cc_start: 0.7721 (tt0) cc_final: 0.7249 (tm-30) REVERT: A 1154 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8211 (ttp) REVERT: A 1196 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.7939 (mtm) REVERT: A 1241 MET cc_start: 0.8774 (mmm) cc_final: 0.8441 (mmm) REVERT: A 1260 ASP cc_start: 0.7494 (t70) cc_final: 0.7191 (t70) REVERT: A 1329 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8769 (pp) REVERT: B 734 LYS cc_start: 0.9192 (ptmt) cc_final: 0.8837 (ttpp) REVERT: B 738 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8733 (mm-30) REVERT: B 742 LEU cc_start: 0.9623 (OUTLIER) cc_final: 0.9394 (mm) REVERT: B 748 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7851 (mm-30) outliers start: 34 outliers final: 20 residues processed: 113 average time/residue: 0.2405 time to fit residues: 38.1411 Evaluate side-chains 104 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 77 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 545 THR 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 714 VAL Chi-restraints excluded: chain A residue 725 TRP Chi-restraints excluded: chain A residue 787 ASP Chi-restraints excluded: chain A residue 823 GLU Chi-restraints excluded: chain A residue 825 LEU 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 933 HIS Chi-restraints excluded: chain A residue 964 HIS Chi-restraints excluded: chain A residue 1022 MET 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 1154 MET Chi-restraints excluded: chain A residue 1196 MET Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1243 VAL Chi-restraints excluded: chain A residue 1258 TRP 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 9805 Z= 0.323 Angle : 0.748 12.607 13592 Z= 0.378 Chirality : 0.044 0.179 1527 Planarity : 0.005 0.049 1495 Dihedral : 16.667 74.045 2150 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 4.40 % Allowed : 21.21 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.27), residues: 955 helix: -0.06 (0.24), residues: 464 sheet: -1.84 (0.58), residues: 72 loop : -2.84 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 725 HIS 0.005 0.001 HIS A1026 PHE 0.039 0.002 PHE A1252 TYR 0.017 0.002 TYR A1081 ARG 0.009 0.001 ARG C 746 *********************** 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 122 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 84 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 MET cc_start: 0.8322 (tmm) cc_final: 0.7966 (tmm) REVERT: A 573 HIS cc_start: 0.8188 (OUTLIER) cc_final: 0.7535 (t-90) REVERT: A 697 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8594 (tt) REVERT: A 823 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8313 (mt-10) REVERT: A 1005 GLN cc_start: 0.8201 (pt0) cc_final: 0.7948 (pt0) REVERT: A 1036 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8182 (mm) REVERT: A 1111 GLU cc_start: 0.7755 (tt0) cc_final: 0.7338 (tm-30) REVERT: A 1154 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8252 (ttp) REVERT: A 1217 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8954 (mm) REVERT: A 1241 MET cc_start: 0.8793 (mmm) cc_final: 0.8477 (mmm) REVERT: A 1329 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8800 (pp) REVERT: B 734 LYS cc_start: 0.9249 (ptmt) cc_final: 0.8897 (ptmm) REVERT: B 738 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8638 (mm-30) REVERT: B 742 LEU cc_start: 0.9601 (OUTLIER) cc_final: 0.9366 (mm) REVERT: B 748 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7841 (mm-30) REVERT: C 740 LYS cc_start: 0.9473 (tptm) cc_final: 0.9253 (ttpp) outliers start: 38 outliers final: 24 residues processed: 113 average time/residue: 0.2133 time to fit residues: 34.2045 Evaluate side-chains 111 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 79 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 573 HIS Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 725 TRP Chi-restraints excluded: chain A residue 787 ASP Chi-restraints excluded: chain A residue 823 GLU Chi-restraints excluded: chain A residue 825 LEU 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 920 CYS Chi-restraints excluded: chain A residue 933 HIS Chi-restraints excluded: chain A residue 964 HIS Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain A residue 1036 LEU 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 1154 MET Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1243 VAL Chi-restraints excluded: chain A residue 1258 TRP Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1329 LEU Chi-restraints excluded: chain A residue 1357 TRP Chi-restraints excluded: chain B residue 736 GLN Chi-restraints excluded: chain B residue 742 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 48 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 94 optimal weight: 0.0040 chunk 85 optimal weight: 0.7980 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1256 GLN ** A1266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9805 Z= 0.182 Angle : 0.701 13.948 13592 Z= 0.345 Chirality : 0.041 0.233 1527 Planarity : 0.004 0.052 1495 Dihedral : 16.508 73.818 2150 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 3.48 % Allowed : 23.06 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.27), residues: 955 helix: 0.12 (0.24), residues: 463 sheet: -2.06 (0.59), residues: 70 loop : -2.66 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 725 HIS 0.006 0.001 HIS A1026 PHE 0.042 0.001 PHE A1252 TYR 0.013 0.001 TYR A 784 ARG 0.004 0.000 ARG A 687 *********************** 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 124 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 94 time to evaluate : 1.037 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: A 573 HIS cc_start: 0.7771 (OUTLIER) cc_final: 0.7143 (t-90) REVERT: A 1011 MET cc_start: 0.8690 (ttm) cc_final: 0.8478 (tmm) REVERT: A 1111 GLU cc_start: 0.7577 (tt0) cc_final: 0.7051 (tm-30) REVERT: A 1241 MET cc_start: 0.8384 (mmm) cc_final: 0.7948 (mmm) REVERT: A 1285 LYS cc_start: 0.8808 (mmmt) cc_final: 0.8598 (mmmt) REVERT: B 734 LYS cc_start: 0.9222 (ptmt) cc_final: 0.8947 (ttpp) REVERT: B 742 LEU cc_start: 0.9618 (OUTLIER) cc_final: 0.9393 (mm) REVERT: B 748 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7843 (mm-30) outliers start: 30 outliers final: 17 residues processed: 116 average time/residue: 0.2228 time to fit residues: 36.0870 Evaluate side-chains 101 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 714 VAL Chi-restraints excluded: chain A residue 725 TRP Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 891 CYS Chi-restraints excluded: chain A residue 920 CYS Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1036 LEU 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 1154 MET Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1256 GLN Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain A residue 1357 TRP Chi-restraints excluded: chain B residue 742 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 82 optimal weight: 0.3980 chunk 86 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 chunk 96 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1256 GLN A1264 GLN ** A1266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9805 Z= 0.187 Angle : 0.724 14.726 13592 Z= 0.352 Chirality : 0.041 0.225 1527 Planarity : 0.004 0.053 1495 Dihedral : 16.478 73.882 2150 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 2.67 % Allowed : 24.33 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.28), residues: 955 helix: 0.18 (0.25), residues: 470 sheet: -1.93 (0.60), residues: 70 loop : -2.61 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 725 HIS 0.005 0.001 HIS A1026 PHE 0.039 0.001 PHE A1252 TYR 0.011 0.001 TYR A 784 ARG 0.006 0.000 ARG A 517 *********************** 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 113 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 90 time to evaluate : 1.125 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 530 MET cc_start: 0.8522 (tmm) cc_final: 0.8211 (tmm) REVERT: A 573 HIS cc_start: 0.7840 (OUTLIER) cc_final: 0.6938 (t-90) REVERT: A 897 MET cc_start: 0.7857 (mmm) cc_final: 0.7593 (mmm) REVERT: A 908 MET cc_start: 0.6970 (tmm) cc_final: 0.6508 (tmm) REVERT: A 977 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7424 (mt-10) REVERT: A 1011 MET cc_start: 0.8745 (ttm) cc_final: 0.8519 (tmm) REVERT: A 1111 GLU cc_start: 0.7534 (tt0) cc_final: 0.6993 (tm-30) REVERT: A 1154 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8067 (ttp) REVERT: A 1241 MET cc_start: 0.8386 (mmm) cc_final: 0.7935 (mmm) REVERT: B 742 LEU cc_start: 0.9605 (OUTLIER) cc_final: 0.9402 (mm) REVERT: B 748 GLU cc_start: 0.8309 (tm-30) cc_final: 0.7849 (mm-30) outliers start: 23 outliers final: 15 residues processed: 108 average time/residue: 0.2406 time to fit residues: 36.6382 Evaluate side-chains 98 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 714 VAL Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 891 CYS Chi-restraints excluded: chain A residue 920 CYS Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1036 LEU 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 1154 MET Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1256 GLN Chi-restraints excluded: chain A residue 1309 ILE Chi-restraints excluded: chain B residue 736 GLN Chi-restraints excluded: chain B residue 742 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 24 optimal weight: 0.0570 chunk 74 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1256 GLN ** A1266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9805 Z= 0.191 Angle : 0.736 15.035 13592 Z= 0.357 Chirality : 0.041 0.214 1527 Planarity : 0.004 0.047 1495 Dihedral : 16.467 73.881 2150 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 2.32 % Allowed : 24.68 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.28), residues: 955 helix: 0.17 (0.24), residues: 470 sheet: -1.78 (0.62), residues: 70 loop : -2.52 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP A 725 HIS 0.005 0.001 HIS A1026 PHE 0.040 0.001 PHE A1252 TYR 0.011 0.001 TYR A 784 ARG 0.005 0.000 ARG A 517 ********************** 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 109 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 89 time to evaluate : 0.969 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 522 LEU cc_start: 0.7979 (mm) cc_final: 0.7438 (pp) REVERT: A 530 MET cc_start: 0.8520 (tmm) cc_final: 0.8216 (tmm) REVERT: A 573 HIS cc_start: 0.7559 (OUTLIER) cc_final: 0.6974 (t-90) REVERT: A 897 MET cc_start: 0.7842 (mmm) cc_final: 0.7586 (mmm) REVERT: A 908 MET cc_start: 0.7322 (tmm) cc_final: 0.6772 (tmm) REVERT: A 1011 MET cc_start: 0.8768 (ttm) cc_final: 0.8490 (tmm) REVERT: A 1036 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8235 (mm) REVERT: A 1111 GLU cc_start: 0.7542 (tt0) cc_final: 0.7162 (tm-30) REVERT: A 1241 MET cc_start: 0.8348 (mmm) cc_final: 0.7901 (mmm) REVERT: B 748 GLU cc_start: 0.8344 (tm-30) cc_final: 0.7884 (mm-30) outliers start: 20 outliers final: 12 residues processed: 104 average time/residue: 0.2208 time to fit residues: 32.2090 Evaluate side-chains 97 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 83 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 714 VAL Chi-restraints excluded: chain A residue 725 TRP Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 891 CYS Chi-restraints excluded: chain A residue 920 CYS Chi-restraints excluded: chain A residue 1018 LEU 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 1202 THR Chi-restraints excluded: chain A residue 1309 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 10 optimal weight: 0.0000 chunk 14 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 58 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** A1087 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 = 0.3400 r_free = 0.3400 target = 0.061862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.050566 restraints weight = 48290.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.052064 restraints weight = 28767.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.053087 restraints weight = 19929.201| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9805 Z= 0.215 Angle : 0.743 14.836 13592 Z= 0.363 Chirality : 0.042 0.208 1527 Planarity : 0.004 0.046 1495 Dihedral : 16.470 73.952 2150 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 1.85 % Allowed : 25.14 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.28), residues: 955 helix: 0.13 (0.24), residues: 476 sheet: -1.81 (0.61), residues: 70 loop : -2.56 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP A 725 HIS 0.005 0.001 HIS A1026 PHE 0.040 0.002 PHE A1252 TYR 0.012 0.001 TYR A 784 ARG 0.006 0.000 ARG C 746 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1730.04 seconds wall clock time: 31 minutes 53.74 seconds (1913.74 seconds total)