Starting phenix.real_space_refine on Thu Nov 16 09:35:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lxd_30005/11_2023/6lxd_30005.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lxd_30005/11_2023/6lxd_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_30005/11_2023/6lxd_30005.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lxd_30005/11_2023/6lxd_30005.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lxd_30005/11_2023/6lxd_30005.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lxd_30005/11_2023/6lxd_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-1.21rc1-5144/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: 6.11, 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 - 3.50 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: 4.33 Conformation dependent library (CDL) restraints added in 1.4 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: 3.30 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: 3.55 Time building geometry restraints manager: 4.46 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: 5209 17.50 - 35.00: 453 35.00 - 52.50: 95 52.50 - 70.00: 28 70.00 - 87.50: 5 Dihedral angle restraints: 5790 sinusoidal: 2962 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 5787 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: 0.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.000 Extract box with map and model: 1.760 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 33.180 Find NCS groups from input model: 0.230 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.650 ------------------------------------------------------------------------------- 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 : 13.461 87.502 3954 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 0.70 % Allowed : 5.56 % Favored : 93.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 *********************** 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 : 1.016 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 outliers start: 6 outliers final: 1 residues processed: 168 average time/residue: 0.2878 time to fit residues: 63.4805 Evaluate side-chains 93 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 1.018 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0889 time to fit residues: 1.4320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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 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** A1222 GLN ** A1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1318 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9805 Z= 0.254 Angle : 0.658 9.667 13592 Z= 0.331 Chirality : 0.040 0.219 1527 Planarity : 0.005 0.056 1495 Dihedral : 9.261 67.968 1918 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 2.32 % Allowed : 15.41 % Favored : 82.27 % 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: -2.37 (0.27), residues: 955 helix: 0.00 (0.24), residues: 455 sheet: -2.65 (0.57), residues: 72 loop : -3.24 (0.28), residues: 428 *********************** 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 121 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 101 time to evaluate : 1.047 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 outliers start: 20 outliers final: 10 residues processed: 115 average time/residue: 0.2673 time to fit residues: 41.8105 Evaluate side-chains 95 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 1.065 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1059 time to fit residues: 3.3092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 63 optimal weight: 0.2980 chunk 25 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 100 optimal weight: 8.9990 chunk 82 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 936 HIS A1170 HIS A1197 GLN ** A1266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 736 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9805 Z= 0.167 Angle : 0.605 11.423 13592 Z= 0.299 Chirality : 0.038 0.141 1527 Planarity : 0.004 0.051 1495 Dihedral : 9.106 66.986 1918 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 1.16 % Allowed : 18.66 % Favored : 80.19 % 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: -2.04 (0.27), residues: 955 helix: 0.36 (0.25), residues: 460 sheet: -2.46 (0.58), residues: 72 loop : -3.22 (0.28), residues: 423 *********************** 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 119 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 0.947 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 outliers start: 10 outliers final: 5 residues processed: 115 average time/residue: 0.2832 time to fit residues: 43.3775 Evaluate side-chains 94 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 89 time to evaluate : 1.098 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1032 time to fit residues: 2.3309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 44 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 chunk 26 optimal weight: 0.0170 chunk 82 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 overall best weight: 2.8024 ------------------------------------------------------------------------------- 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** A 826 GLN A 902 HIS A1222 GLN A1242 ASN ** A1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3120 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= 0.282 Angle : 0.683 11.133 13592 Z= 0.344 Chirality : 0.041 0.180 1527 Planarity : 0.005 0.058 1495 Dihedral : 9.352 68.316 1918 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 21.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 2.55 % Allowed : 20.05 % Favored : 77.40 % 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: 0.21 (0.24), residues: 461 sheet: -2.20 (0.56), residues: 72 loop : -3.05 (0.28), residues: 422 *********************** 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 119 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 97 time to evaluate : 1.059 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 outliers start: 22 outliers final: 7 residues processed: 111 average time/residue: 0.2606 time to fit residues: 39.5649 Evaluate side-chains 89 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 82 time to evaluate : 0.954 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1092 time to fit residues: 2.6816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 40 optimal weight: 7.9990 chunk 84 optimal weight: 20.0000 chunk 68 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 overall best weight: 2.9386 ------------------------------------------------------------------------------- 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** ** A1267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3605 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= 0.289 Angle : 0.710 11.160 13592 Z= 0.356 Chirality : 0.041 0.149 1527 Planarity : 0.005 0.055 1495 Dihedral : 9.499 68.457 1918 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 2.32 % Allowed : 21.67 % 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: -1.94 (0.27), residues: 955 helix: 0.16 (0.24), residues: 463 sheet: -1.96 (0.58), residues: 72 loop : -2.92 (0.29), residues: 420 *********************** 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 110 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 90 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 outliers start: 20 outliers final: 9 residues processed: 105 average time/residue: 0.2435 time to fit residues: 35.7652 Evaluate side-chains 90 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 81 time to evaluate : 1.029 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1078 time to fit residues: 3.0489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 98 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 0.0970 chunk 8 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 95 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- 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** ** A1267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3824 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= 0.264 Angle : 0.703 12.460 13592 Z= 0.351 Chirality : 0.042 0.196 1527 Planarity : 0.005 0.056 1495 Dihedral : 9.521 68.115 1918 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 22.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 1.85 % Allowed : 23.06 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.89 (0.27), residues: 955 helix: 0.12 (0.24), residues: 471 sheet: -1.85 (0.58), residues: 72 loop : -2.85 (0.30), residues: 412 *********************** 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 106 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 3 residues processed: 104 average time/residue: 0.2527 time to fit residues: 36.5635 Evaluate side-chains 85 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 82 time to evaluate : 0.951 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0925 time to fit residues: 1.7622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 0.1980 chunk 55 optimal weight: 0.0980 chunk 83 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 761 GLN A1222 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: 0.7982 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9805 Z= 0.175 Angle : 0.677 13.615 13592 Z= 0.331 Chirality : 0.040 0.217 1527 Planarity : 0.004 0.050 1495 Dihedral : 9.277 66.143 1918 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 1.51 % Allowed : 24.33 % Favored : 74.16 % 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: -1.66 (0.27), residues: 955 helix: 0.37 (0.24), residues: 466 sheet: -1.79 (0.58), residues: 72 loop : -2.77 (0.29), residues: 417 *********************** 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 116 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 1.028 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 outliers start: 13 outliers final: 7 residues processed: 112 average time/residue: 0.2710 time to fit residues: 41.4576 Evaluate side-chains 88 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 81 time to evaluate : 1.024 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1060 time to fit residues: 2.7181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.0050 chunk 62 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 94 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 7.9990 overall best weight: 2.7600 ------------------------------------------------------------------------------- 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** A1222 GLN ** A1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1267 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.4071 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= 0.274 Angle : 0.743 13.278 13592 Z= 0.370 Chirality : 0.043 0.207 1527 Planarity : 0.005 0.053 1495 Dihedral : 9.377 69.993 1918 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 22.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 1.16 % Allowed : 24.45 % 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: -1.73 (0.27), residues: 955 helix: 0.19 (0.24), residues: 471 sheet: -1.67 (0.59), residues: 72 loop : -2.72 (0.30), residues: 412 *********************** 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 96 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 93 average time/residue: 0.2497 time to fit residues: 33.5481 Evaluate side-chains 85 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 79 time to evaluate : 1.395 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2185 time to fit residues: 3.6018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 82 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 96 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- 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 761 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: 0.8037 moved from start: 0.4157 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 : 0.741 13.754 13592 Z= 0.369 Chirality : 0.043 0.223 1527 Planarity : 0.005 0.048 1495 Dihedral : 9.307 70.331 1918 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 20.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 0.81 % Allowed : 25.03 % Favored : 74.16 % 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: -1.74 (0.27), residues: 955 helix: 0.15 (0.24), residues: 470 sheet: -1.60 (0.59), residues: 72 loop : -2.69 (0.30), residues: 413 *********************** 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 95 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 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: symmetry clash outliers start: 7 outliers final: 3 residues processed: 95 average time/residue: 0.2266 time to fit residues: 30.6846 Evaluate side-chains 83 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 80 time to evaluate : 1.057 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1116 time to fit residues: 1.9448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0670 chunk 80 optimal weight: 0.0270 chunk 8 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 761 GLN A1222 GLN A1266 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9805 Z= 0.187 Angle : 0.751 14.892 13592 Z= 0.367 Chirality : 0.042 0.215 1527 Planarity : 0.004 0.049 1495 Dihedral : 9.177 70.211 1918 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 0.46 % Allowed : 25.61 % Favored : 73.93 % 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: -1.63 (0.28), residues: 955 helix: 0.24 (0.24), residues: 472 sheet: -1.54 (0.60), residues: 72 loop : -2.65 (0.30), residues: 411 ********************** 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 97 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 93 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 96 average time/residue: 0.2285 time to fit residues: 31.2626 Evaluate side-chains 83 residues out of total 865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 1.034 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1249 time to fit residues: 1.5410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 33 optimal weight: 7.9990 chunk 83 optimal weight: 0.1980 chunk 10 optimal weight: 0.0040 chunk 14 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 overall best weight: 1.6396 ------------------------------------------------------------------------------- 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 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1222 GLN ** A1361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.062034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.050703 restraints weight = 47961.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.052224 restraints weight = 28283.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.053256 restraints weight = 19478.942| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9805 Z= 0.216 Angle : 0.755 15.523 13592 Z= 0.374 Chirality : 0.042 0.206 1527 Planarity : 0.005 0.049 1495 Dihedral : 9.203 72.747 1918 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 0.35 % Allowed : 26.54 % 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: -1.55 (0.28), residues: 955 helix: 0.31 (0.24), residues: 470 sheet: -1.49 (0.60), residues: 72 loop : -2.61 (0.30), residues: 413 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1782.44 seconds wall clock time: 33 minutes 37.78 seconds (2017.78 seconds total)