Starting phenix.real_space_refine on Fri Feb 16 09:40:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lxd_30005/02_2024/6lxd_30005.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lxd_30005/02_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_30005/02_2024/6lxd_30005.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lxd_30005/02_2024/6lxd_30005.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lxd_30005/02_2024/6lxd_30005.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lxd_30005/02_2024/6lxd_30005.pdb" } 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 Residue "A ARG 414": "NH1" <-> "NH2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A GLU 507": "OE1" <-> "OE2" Residue "A ARG 544": "NH1" <-> "NH2" Residue "A ARG 548": "NH1" <-> "NH2" Residue "A ARG 622": "NH1" <-> "NH2" Residue "A ARG 759": "NH1" <-> "NH2" Residue "A PHE 775": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 778": "NH1" <-> "NH2" Residue "A ARG 835": "NH1" <-> "NH2" Residue "A ARG 853": "NH1" <-> "NH2" Residue "A ARG 930": "NH1" <-> "NH2" Residue "A ARG 938": "NH1" <-> "NH2" Residue "A GLU 966": "OE1" <-> "OE2" Residue "A GLU 969": "OE1" <-> "OE2" Residue "A GLU 977": "OE1" <-> "OE2" Residue "A GLU 992": "OE1" <-> "OE2" Residue "A ARG 1032": "NH1" <-> "NH2" Residue "A GLU 1109": "OE1" <-> "OE2" Residue "A ARG 1213": "NH1" <-> "NH2" Residue "A GLU 1235": "OE1" <-> "OE2" Residue "A ARG 1248": "NH1" <-> "NH2" Residue "A ARG 1273": "NH1" <-> "NH2" Residue "A ARG 1296": "NH1" <-> "NH2" Residue "A ARG 1308": "NH1" <-> "NH2" Residue "B GLU 747": "OE1" <-> "OE2" Residue "C ARG 746": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 5.45, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 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: 4.40 Conformation dependent library (CDL) restraints added in 1.5 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: 3.13 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: 3.51 Time building geometry restraints manager: 4.66 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: 100.20 - 106.96: 699 106.96 - 113.71: 5499 113.71 - 120.46: 3823 120.46 - 127.22: 3321 127.22 - 133.97: 250 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 2.440 nonbonded pdb=" O ILE A 772 " pdb=" OG SER A 844 " model vdw 2.242 2.440 nonbonded pdb=" OH TYR A1024 " pdb=" O LEU A1030 " model vdw 2.246 2.440 nonbonded pdb=" O ARG A1126 " pdb=" OG1 THR A1129 " model vdw 2.272 2.440 nonbonded pdb=" O LYS A 559 " pdb=" NH2 ARG A 570 " model vdw 2.281 2.520 ... (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 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: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.000 Extract box with map and model: 1.720 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 32.280 Find NCS groups from input model: 0.320 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.580 ------------------------------------------------------------------------------- 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 : 0.913 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: 0.2762 time to fit residues: 60.5195 Evaluate side-chains 101 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 99 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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: 9.9990 chunk 77 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 GLN 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** ** A1266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1318 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9805 Z= 0.298 Angle : 0.690 8.145 13592 Z= 0.350 Chirality : 0.041 0.152 1527 Planarity : 0.005 0.058 1495 Dihedral : 16.932 74.420 2152 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 22.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.74 % Favored : 90.16 % Rotamer: Outliers : 2.32 % Allowed : 15.53 % Favored : 82.16 % 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: -2.55 (0.26), residues: 955 helix: -0.16 (0.23), residues: 460 sheet: -2.66 (0.56), residues: 72 loop : -3.36 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 412 HIS 0.009 0.002 HIS A1026 PHE 0.027 0.002 PHE A 762 TYR 0.014 0.002 TYR A1081 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 123 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 103 time to evaluate : 0.992 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 438 THR cc_start: 0.6506 (OUTLIER) cc_final: 0.6269 (t) REVERT: A 564 MET cc_start: 0.7554 (pmm) cc_final: 0.7236 (pmm) REVERT: A 823 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8461 (mt-10) REVERT: A 1154 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.7952 (ttp) REVERT: A 1235 GLU cc_start: 0.8142 (mp0) cc_final: 0.7771 (mp0) REVERT: A 1260 ASP cc_start: 0.7445 (t0) cc_final: 0.6853 (t0) REVERT: A 1357 TRP cc_start: 0.6833 (t-100) cc_final: 0.6569 (t-100) REVERT: B 736 GLN cc_start: 0.8995 (pt0) cc_final: 0.8689 (pt0) REVERT: B 737 GLU cc_start: 0.9094 (mm-30) cc_final: 0.8711 (mm-30) REVERT: B 740 LYS cc_start: 0.8614 (ptmm) cc_final: 0.8007 (ptpp) REVERT: B 742 LEU cc_start: 0.9655 (OUTLIER) cc_final: 0.9304 (mm) REVERT: B 748 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7838 (mm-30) REVERT: C 735 LEU cc_start: 0.9264 (pp) cc_final: 0.9045 (pp) outliers start: 20 outliers final: 11 residues processed: 118 average time/residue: 0.2509 time to fit residues: 40.1709 Evaluate side-chains 96 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 81 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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 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 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 B residue 742 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 82 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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** ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1197 GLN ** A1222 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9805 Z= 0.177 Angle : 0.614 11.052 13592 Z= 0.303 Chirality : 0.039 0.176 1527 Planarity : 0.004 0.056 1495 Dihedral : 16.780 73.865 2151 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 2.67 % Allowed : 17.96 % Favored : 79.37 % 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: -2.00 (0.27), residues: 955 helix: 0.36 (0.24), residues: 460 sheet: -2.53 (0.56), residues: 72 loop : -3.15 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 725 HIS 0.007 0.001 HIS A1026 PHE 0.045 0.001 PHE A1252 TYR 0.013 0.001 TYR A 733 ARG 0.005 0.000 ARG A 687 *********************** 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 135 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 112 time to evaluate : 0.895 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: A 564 MET cc_start: 0.7546 (pmm) cc_final: 0.7147 (pmm) REVERT: A 573 HIS cc_start: 0.7778 (OUTLIER) cc_final: 0.6759 (t-90) REVERT: A 823 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8513 (mt-10) REVERT: A 1241 MET cc_start: 0.8686 (mmm) cc_final: 0.8196 (mmm) REVERT: A 1260 ASP cc_start: 0.7197 (t0) cc_final: 0.6942 (t0) REVERT: A 1329 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8670 (pp) REVERT: A 1357 TRP cc_start: 0.6861 (t-100) cc_final: 0.6587 (t-100) REVERT: B 735 LEU cc_start: 0.9118 (mt) cc_final: 0.8570 (mm) REVERT: B 736 GLN cc_start: 0.8978 (pt0) cc_final: 0.8655 (pt0) REVERT: B 737 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8681 (mm-30) REVERT: B 740 LYS cc_start: 0.8639 (ptmm) cc_final: 0.8000 (ptpp) REVERT: B 742 LEU cc_start: 0.9638 (mm) cc_final: 0.9258 (mm) REVERT: B 748 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7885 (mm-30) outliers start: 23 outliers final: 15 residues processed: 130 average time/residue: 0.2497 time to fit residues: 44.2436 Evaluate side-chains 111 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 93 time to evaluate : 1.023 ------------------------------------------------------------------------------- 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 613 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 933 HIS Chi-restraints excluded: chain A residue 1036 LEU Chi-restraints excluded: chain A residue 1057 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 1309 ILE Chi-restraints excluded: chain A residue 1329 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 69 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 44 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 88 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 GLN A 902 HIS ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 736 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9805 Z= 0.284 Angle : 0.698 12.304 13592 Z= 0.349 Chirality : 0.041 0.155 1527 Planarity : 0.005 0.058 1495 Dihedral : 16.758 74.103 2150 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 22.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 4.17 % Allowed : 19.81 % Favored : 76.01 % 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: -1.87 (0.27), residues: 955 helix: 0.29 (0.24), residues: 462 sheet: -2.19 (0.56), residues: 72 loop : -2.93 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 725 HIS 0.007 0.001 HIS A 630 PHE 0.050 0.002 PHE A1252 TYR 0.015 0.002 TYR A 733 ARG 0.004 0.001 ARG A1122 *********************** 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 134 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 98 time to evaluate : 1.001 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: 0.8123 (OUTLIER) cc_final: 0.7518 (t-90) REVERT: A 755 ASP cc_start: 0.7146 (OUTLIER) cc_final: 0.6837 (p0) REVERT: A 823 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8435 (mt-10) REVERT: A 905 ASN cc_start: 0.7052 (p0) cc_final: 0.6748 (p0) REVERT: A 949 MET cc_start: 0.8677 (mtp) cc_final: 0.8339 (mtp) REVERT: A 1036 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8316 (mm) REVERT: A 1235 GLU cc_start: 0.8199 (mp0) cc_final: 0.7794 (mp0) REVERT: A 1329 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8730 (pp) REVERT: A 1355 MET cc_start: 0.8375 (mtt) cc_final: 0.7874 (mmt) REVERT: A 1357 TRP cc_start: 0.6731 (t-100) cc_final: 0.6371 (t-100) REVERT: B 735 LEU cc_start: 0.9264 (mt) cc_final: 0.8754 (mt) REVERT: B 742 LEU cc_start: 0.9615 (OUTLIER) cc_final: 0.9296 (mm) REVERT: B 748 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7900 (mm-30) REVERT: C 735 LEU cc_start: 0.9158 (pp) cc_final: 0.8947 (pp) REVERT: C 740 LYS cc_start: 0.9452 (tptm) cc_final: 0.9171 (ttpp) REVERT: C 746 ARG cc_start: 0.8483 (ptm160) cc_final: 0.8226 (ptm160) outliers start: 36 outliers final: 20 residues processed: 127 average time/residue: 0.2209 time to fit residues: 39.5938 Evaluate side-chains 112 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 86 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 573 HIS 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 755 ASP 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 958 THR 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 1202 THR Chi-restraints excluded: chain A residue 1243 VAL Chi-restraints excluded: chain A residue 1259 ASN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 84 optimal weight: 0.7980 chunk 68 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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** ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1222 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9805 Z= 0.244 Angle : 0.680 10.540 13592 Z= 0.338 Chirality : 0.041 0.223 1527 Planarity : 0.005 0.053 1495 Dihedral : 16.711 73.959 2150 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 21.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 4.87 % Allowed : 19.93 % 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: -1.73 (0.27), residues: 955 helix: 0.36 (0.24), residues: 463 sheet: -1.98 (0.56), residues: 72 loop : -2.82 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 725 HIS 0.006 0.001 HIS A 630 PHE 0.048 0.002 PHE A1252 TYR 0.013 0.001 TYR A 784 ARG 0.004 0.000 ARG A 687 *********************** 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 138 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 96 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 573 HIS cc_start: 0.8112 (OUTLIER) cc_final: 0.7129 (t-90) REVERT: A 722 MET cc_start: 0.7607 (ppp) cc_final: 0.7345 (ppp) REVERT: A 755 ASP cc_start: 0.6874 (OUTLIER) cc_final: 0.6504 (p0) REVERT: A 823 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8406 (mt-10) REVERT: A 949 MET cc_start: 0.8767 (mtp) cc_final: 0.8557 (mtp) REVERT: A 1005 GLN cc_start: 0.8244 (pt0) cc_final: 0.8033 (pt0) REVERT: A 1111 GLU cc_start: 0.7722 (tt0) cc_final: 0.7141 (tm-30) REVERT: A 1235 GLU cc_start: 0.8222 (mp0) cc_final: 0.7852 (mp0) REVERT: A 1241 MET cc_start: 0.8776 (mmm) cc_final: 0.8205 (mmm) REVERT: A 1329 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8784 (pp) REVERT: A 1355 MET cc_start: 0.8339 (mtt) cc_final: 0.7961 (mmt) REVERT: A 1357 TRP cc_start: 0.6800 (t-100) cc_final: 0.6290 (t-100) REVERT: B 742 LEU cc_start: 0.9612 (OUTLIER) cc_final: 0.9322 (mm) REVERT: B 748 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7891 (mm-30) REVERT: C 740 LYS cc_start: 0.9422 (tptm) cc_final: 0.9069 (ttpp) REVERT: C 746 ARG cc_start: 0.8335 (ptm160) cc_final: 0.8098 (ptm160) outliers start: 42 outliers final: 23 residues processed: 127 average time/residue: 0.2199 time to fit residues: 39.0339 Evaluate side-chains 110 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 82 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 573 HIS Chi-restraints excluded: chain A residue 600 ILE 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 755 ASP Chi-restraints excluded: chain A residue 765 ASP 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 933 HIS Chi-restraints excluded: chain A residue 958 THR 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 8 optimal weight: 0.2980 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 95 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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** ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1222 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: 0.8045 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9805 Z= 0.240 Angle : 0.688 13.544 13592 Z= 0.340 Chirality : 0.041 0.262 1527 Planarity : 0.005 0.054 1495 Dihedral : 16.687 73.939 2150 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 21.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 4.63 % Allowed : 20.86 % Favored : 74.51 % 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: -1.60 (0.27), residues: 955 helix: 0.43 (0.24), residues: 464 sheet: -1.80 (0.58), residues: 72 loop : -2.73 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 725 HIS 0.006 0.001 HIS A 630 PHE 0.026 0.002 PHE A1252 TYR 0.013 0.001 TYR A 784 ARG 0.003 0.000 ARG A 967 *********************** 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 135 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 95 time to evaluate : 0.902 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: 0.8023 (OUTLIER) cc_final: 0.7237 (t-90) REVERT: A 722 MET cc_start: 0.7662 (ppp) cc_final: 0.7318 (ppp) REVERT: A 755 ASP cc_start: 0.6891 (OUTLIER) cc_final: 0.6526 (p0) REVERT: A 823 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8389 (mt-10) REVERT: A 977 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7350 (mt-10) REVERT: A 1005 GLN cc_start: 0.8184 (pt0) cc_final: 0.7969 (pt0) REVERT: A 1111 GLU cc_start: 0.7844 (tt0) cc_final: 0.7221 (tm-30) REVERT: A 1196 MET cc_start: 0.8401 (mtm) cc_final: 0.8170 (mpp) REVERT: A 1235 GLU cc_start: 0.8237 (mp0) cc_final: 0.7850 (mp0) REVERT: A 1329 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8785 (pp) REVERT: A 1355 MET cc_start: 0.8325 (mtt) cc_final: 0.7799 (mmm) REVERT: A 1357 TRP cc_start: 0.6883 (t-100) cc_final: 0.6253 (t-100) REVERT: B 735 LEU cc_start: 0.9220 (mt) cc_final: 0.8818 (mm) REVERT: B 742 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9340 (mm) REVERT: B 748 GLU cc_start: 0.8344 (tm-30) cc_final: 0.7880 (mm-30) REVERT: C 740 LYS cc_start: 0.9424 (tptm) cc_final: 0.9125 (ttpp) outliers start: 40 outliers final: 26 residues processed: 127 average time/residue: 0.2195 time to fit residues: 38.7675 Evaluate side-chains 116 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 85 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 573 HIS Chi-restraints excluded: chain A residue 600 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 755 ASP Chi-restraints excluded: chain A residue 803 LEU 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 958 THR 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 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 742 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 0.0970 chunk 55 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 761 GLN ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1222 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: 0.8014 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9805 Z= 0.190 Angle : 0.674 12.790 13592 Z= 0.331 Chirality : 0.040 0.207 1527 Planarity : 0.004 0.051 1495 Dihedral : 16.616 73.826 2150 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 4.17 % Allowed : 22.71 % Favored : 73.12 % 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: -1.47 (0.28), residues: 955 helix: 0.51 (0.25), residues: 466 sheet: -1.66 (0.58), residues: 72 loop : -2.66 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 725 HIS 0.006 0.001 HIS A1026 PHE 0.024 0.001 PHE A1252 TYR 0.012 0.001 TYR A 784 ARG 0.006 0.000 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 138 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 102 time to evaluate : 1.039 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 697 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8632 (tt) REVERT: A 722 MET cc_start: 0.7603 (ppp) cc_final: 0.7261 (ppp) REVERT: A 755 ASP cc_start: 0.6784 (OUTLIER) cc_final: 0.6371 (p0) REVERT: A 977 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7303 (mt-10) REVERT: A 1111 GLU cc_start: 0.7762 (tt0) cc_final: 0.7200 (tm-30) REVERT: A 1196 MET cc_start: 0.8437 (mtm) cc_final: 0.7838 (mpp) REVERT: A 1235 GLU cc_start: 0.8139 (mp0) cc_final: 0.7731 (mp0) REVERT: A 1241 MET cc_start: 0.8731 (mmm) cc_final: 0.8263 (mmm) REVERT: A 1329 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8757 (pp) REVERT: A 1357 TRP cc_start: 0.6906 (t-100) cc_final: 0.6200 (t-100) REVERT: B 742 LEU cc_start: 0.9561 (OUTLIER) cc_final: 0.9342 (mm) REVERT: B 748 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7886 (mm-30) REVERT: C 740 LYS cc_start: 0.9397 (tptm) cc_final: 0.9097 (ttpp) outliers start: 36 outliers final: 26 residues processed: 130 average time/residue: 0.2259 time to fit residues: 41.1718 Evaluate side-chains 115 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 85 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 567 ASN 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 755 ASP Chi-restraints excluded: chain A residue 803 LEU 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 958 THR 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 1243 VAL Chi-restraints excluded: chain A residue 1259 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 94 optimal weight: 0.0970 chunk 85 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- 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 ** 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** ** A1267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9805 Z= 0.326 Angle : 0.792 17.450 13592 Z= 0.392 Chirality : 0.045 0.358 1527 Planarity : 0.006 0.054 1495 Dihedral : 16.646 73.970 2150 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 25.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.79 % Favored : 89.21 % Rotamer: Outliers : 4.75 % Allowed : 23.06 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.27), residues: 955 helix: 0.19 (0.24), residues: 470 sheet: -1.63 (0.57), residues: 72 loop : -2.75 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 725 HIS 0.008 0.002 HIS A 630 PHE 0.027 0.002 PHE A1252 TYR 0.040 0.002 TYR A1236 ARG 0.004 0.001 ARG A 442 *********************** 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 131 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 90 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 573 HIS cc_start: 0.8241 (OUTLIER) cc_final: 0.7305 (t-90) REVERT: A 630 HIS cc_start: 0.8557 (OUTLIER) cc_final: 0.7995 (m-70) REVERT: A 722 MET cc_start: 0.7740 (ppp) cc_final: 0.7391 (ppp) REVERT: A 755 ASP cc_start: 0.7170 (OUTLIER) cc_final: 0.6836 (p0) REVERT: A 977 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7298 (mt-10) REVERT: A 1036 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8237 (mm) REVERT: A 1111 GLU cc_start: 0.8092 (tt0) cc_final: 0.7356 (tm-30) REVERT: A 1196 MET cc_start: 0.8450 (mtm) cc_final: 0.7797 (mpp) REVERT: A 1217 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.9005 (mm) REVERT: A 1235 GLU cc_start: 0.8055 (mp0) cc_final: 0.7633 (mp0) REVERT: A 1329 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8787 (pp) REVERT: B 734 LYS cc_start: 0.9176 (ptmm) cc_final: 0.8943 (ttpt) REVERT: B 738 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8745 (mm-30) REVERT: B 742 LEU cc_start: 0.9604 (OUTLIER) cc_final: 0.9373 (mm) REVERT: B 748 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7834 (mm-30) REVERT: C 740 LYS cc_start: 0.9472 (tptm) cc_final: 0.9151 (ttpp) outliers start: 41 outliers final: 29 residues processed: 123 average time/residue: 0.1922 time to fit residues: 34.8073 Evaluate side-chains 117 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 81 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 573 HIS Chi-restraints excluded: chain A residue 600 ILE Chi-restraints excluded: chain A residue 630 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 755 ASP Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 803 LEU 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 958 THR 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 1202 THR 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 B residue 736 GLN 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: 8.9990 chunk 71 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 86 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 chunk 59 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 67 optimal weight: 0.0970 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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** ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1222 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: 0.7997 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9805 Z= 0.181 Angle : 0.724 14.586 13592 Z= 0.348 Chirality : 0.043 0.451 1527 Planarity : 0.004 0.056 1495 Dihedral : 16.538 73.664 2150 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 3.59 % Allowed : 24.91 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.28), residues: 955 helix: 0.44 (0.24), residues: 472 sheet: -1.86 (0.58), residues: 70 loop : -2.55 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 725 HIS 0.006 0.001 HIS A1026 PHE 0.024 0.001 PHE A 669 TYR 0.023 0.001 TYR A1236 ARG 0.004 0.000 ARG C 746 *********************** 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 128 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 97 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 755 ASP cc_start: 0.6831 (OUTLIER) cc_final: 0.6483 (p0) REVERT: A 861 MET cc_start: 0.6938 (mtm) cc_final: 0.6715 (mtm) REVERT: A 977 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7300 (mt-10) REVERT: A 1111 GLU cc_start: 0.7654 (tt0) cc_final: 0.7105 (tm-30) REVERT: A 1140 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8415 (pt) REVERT: A 1196 MET cc_start: 0.8445 (mtm) cc_final: 0.7838 (mpp) REVERT: A 1217 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8979 (mm) REVERT: A 1241 MET cc_start: 0.8443 (mmm) cc_final: 0.8110 (mmm) REVERT: A 1329 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8792 (pp) REVERT: A 1357 TRP cc_start: 0.7115 (t-100) cc_final: 0.6407 (t-100) REVERT: B 738 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8671 (mm-30) REVERT: B 748 GLU cc_start: 0.8333 (tm-30) cc_final: 0.7877 (mm-30) REVERT: C 740 LYS cc_start: 0.9415 (tptm) cc_final: 0.9141 (ttpp) REVERT: C 745 GLU cc_start: 0.8988 (pt0) cc_final: 0.8721 (pt0) outliers start: 31 outliers final: 19 residues processed: 120 average time/residue: 0.2196 time to fit residues: 37.2565 Evaluate side-chains 111 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 88 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 567 ASN Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 714 VAL Chi-restraints excluded: chain A residue 725 TRP Chi-restraints excluded: chain A residue 755 ASP 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 958 THR Chi-restraints excluded: chain A residue 1018 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 1217 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 10.0000 chunk 93 optimal weight: 0.0770 chunk 80 optimal weight: 6.9990 chunk 8 optimal weight: 0.0040 chunk 62 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 overall best weight: 1.5952 ------------------------------------------------------------------------------- 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** ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1222 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9805 Z= 0.208 Angle : 0.757 17.931 13592 Z= 0.361 Chirality : 0.043 0.426 1527 Planarity : 0.005 0.061 1495 Dihedral : 16.526 73.761 2150 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 20.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 3.24 % Allowed : 25.03 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.28), residues: 955 helix: 0.41 (0.24), residues: 472 sheet: -1.54 (0.59), residues: 72 loop : -2.59 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 725 HIS 0.005 0.001 HIS A1026 PHE 0.025 0.002 PHE A 669 TYR 0.031 0.002 TYR A1236 ARG 0.006 0.000 ARG C 746 ********************** 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 116 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 88 time to evaluate : 1.011 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 755 ASP cc_start: 0.6688 (OUTLIER) cc_final: 0.6321 (p0) REVERT: A 977 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7229 (mt-10) REVERT: A 1140 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8422 (pt) REVERT: A 1196 MET cc_start: 0.8447 (mtm) cc_final: 0.7826 (mpp) REVERT: A 1217 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.9000 (mm) REVERT: A 1241 MET cc_start: 0.8597 (mmm) cc_final: 0.8250 (mmm) REVERT: A 1329 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8752 (pp) REVERT: B 748 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7884 (mm-30) REVERT: C 740 LYS cc_start: 0.9404 (tptm) cc_final: 0.9109 (ttpp) REVERT: C 745 GLU cc_start: 0.8942 (pt0) cc_final: 0.8673 (pt0) outliers start: 28 outliers final: 21 residues processed: 110 average time/residue: 0.2153 time to fit residues: 33.6949 Evaluate side-chains 113 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 88 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 567 ASN 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 755 ASP 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 933 HIS Chi-restraints excluded: chain A residue 958 THR Chi-restraints excluded: chain A residue 1018 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 1217 LEU 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 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: 0.2980 chunk 33 optimal weight: 0.0870 chunk 83 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 overall best weight: 1.2762 ------------------------------------------------------------------------------- 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** ** A1170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1222 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 = 0.3412 r_free = 0.3412 target = 0.062193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.050983 restraints weight = 48732.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.052362 restraints weight = 29398.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.053268 restraints weight = 20756.968| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9805 Z= 0.194 Angle : 0.740 14.939 13592 Z= 0.353 Chirality : 0.043 0.412 1527 Planarity : 0.005 0.062 1495 Dihedral : 16.503 73.714 2150 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 3.01 % Allowed : 25.72 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.28), residues: 955 helix: 0.46 (0.24), residues: 472 sheet: -1.48 (0.60), residues: 72 loop : -2.57 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 725 HIS 0.005 0.001 HIS A1026 PHE 0.025 0.001 PHE A 669 TYR 0.027 0.001 TYR A1236 ARG 0.007 0.000 ARG C 746 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1737.63 seconds wall clock time: 32 minutes 54.85 seconds (1974.85 seconds total)