Starting phenix.real_space_refine on Wed Aug 5 16:58:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wmi_37653/08_2026/8wmi_37653.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wmi_37653/08_2026/8wmi_37653.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wmi_37653/08_2026/8wmi_37653.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wmi_37653/08_2026/8wmi_37653.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wmi_37653/08_2026/8wmi_37653.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wmi_37653/08_2026/8wmi_37653.map" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 39 5.49 5 S 48 5.16 5 C 6661 2.51 5 N 1910 2.21 5 O 2101 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10763 Number of models: 1 Model: "" Number of chains: 3 Chain: "R" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 826 Classifications: {'RNA': 39} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 7, 'rna3p_pur': 5, 'rna3p_pyr': 14} Link IDs: {'rna2p': 19, 'rna3p': 19} Chain: "A" Number of atoms: 9933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1237, 9933 Classifications: {'peptide': 1237} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 69, 'TRANS': 1167} Chain breaks: 10 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1530 SG CYS A 86 31.106 61.179 143.315 1.00167.47 S ATOM 1776 SG CYS A 115 30.437 63.002 146.580 1.00183.20 S ATOM 1838 SG CYS A 123 33.359 64.123 144.339 1.00164.06 S ATOM 1862 SG CYS A 126 30.196 64.876 143.087 1.00164.08 S ATOM 3939 SG CYS A 463 26.495 43.368 117.825 1.00 97.81 S ATOM 4001 SG CYS A 472 25.737 44.730 121.212 1.00117.18 S ATOM 4015 SG CYS A 474 28.393 41.977 120.839 1.00106.05 S ATOM 4037 SG CYS A 477 29.080 45.542 119.770 1.00100.36 S ATOM 5851 SG CYS A 706 16.732 34.431 91.751 1.00112.69 S ATOM 5866 SG CYS A 708 17.689 31.234 90.060 1.00 99.20 S ATOM 5888 SG CYS A 711 20.376 33.929 90.899 1.00 90.76 S ATOM 7751 SG CYS A 965 23.001 39.486 53.614 1.00 78.96 S ATOM 8629 SG CYS A1312 19.545 40.974 54.239 1.00 87.57 S ATOM 8661 SG CYS A1342 22.140 37.284 54.682 1.00 78.23 S Time building chain proxies: 2.40, per 1000 atoms: 0.22 Number of scatterers: 10763 At special positions: 0 Unit cell: (80.75, 95.2, 159.8, 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 4 29.99 S 48 16.00 P 39 15.00 O 2101 8.00 N 1910 7.00 C 6661 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 520.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 123 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 126 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 86 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 115 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 472 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 463 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 474 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 477 " pdb=" ZN A1703 " pdb="ZN ZN A1703 " - pdb=" ND1 HIS A 703 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 706 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 708 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 711 " pdb=" ZN A1704 " pdb="ZN ZN A1704 " - pdb=" SG CYS A 965 " pdb="ZN ZN A1704 " - pdb=" SG CYS A1312 " pdb="ZN ZN A1704 " - pdb=" SG CYS A1342 " Number of angles added : 15 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2290 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 17 sheets defined 28.8% alpha, 15.7% beta 0 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 22 through 26 removed outlier: 3.559A pdb=" N ARG A 25 " --> pdb=" O GLU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 36 Processing helix chain 'A' and resid 57 through 76 removed outlier: 4.080A pdb=" N LEU A 61 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 163 through 168 Processing helix chain 'A' and resid 211 through 225 removed outlier: 3.650A pdb=" N ARG A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 277 Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 292 through 294 No H-bonds generated for 'chain 'A' and resid 292 through 294' Processing helix chain 'A' and resid 295 through 299 removed outlier: 3.920A pdb=" N LEU A 298 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL A 299 " --> pdb=" O SER A 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 295 through 299' Processing helix chain 'A' and resid 329 through 338 Processing helix chain 'A' and resid 344 through 364 Processing helix chain 'A' and resid 443 through 460 removed outlier: 3.628A pdb=" N VAL A 447 " --> pdb=" O PRO A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 481 Processing helix chain 'A' and resid 542 through 555 Processing helix chain 'A' and resid 586 through 594 Processing helix chain 'A' and resid 595 through 598 removed outlier: 3.874A pdb=" N ARG A 598 " --> pdb=" O TRP A 595 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 595 through 598' Processing helix chain 'A' and resid 599 through 608 Processing helix chain 'A' and resid 643 through 648 removed outlier: 3.683A pdb=" N VAL A 648 " --> pdb=" O ARG A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 691 removed outlier: 3.804A pdb=" N ILE A 690 " --> pdb=" O ALA A 686 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N HIS A 691 " --> pdb=" O VAL A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 715 Processing helix chain 'A' and resid 780 through 785 Processing helix chain 'A' and resid 785 through 801 removed outlier: 3.817A pdb=" N CYS A 789 " --> pdb=" O ASP A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 962 removed outlier: 4.027A pdb=" N LEU A 950 " --> pdb=" O PRO A 946 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 957 " --> pdb=" O MET A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 1232 through 1245 removed outlier: 3.826A pdb=" N ILE A1236 " --> pdb=" O GLU A1232 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS A1237 " --> pdb=" O LYS A1233 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ARG A1243 " --> pdb=" O LYS A1239 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL A1244 " --> pdb=" O GLU A1240 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR A1245 " --> pdb=" O LEU A1241 " (cutoff:3.500A) Processing helix chain 'A' and resid 1300 through 1304 Processing helix chain 'A' and resid 1342 through 1349 Processing helix chain 'A' and resid 1395 through 1399 removed outlier: 3.584A pdb=" N TRP A1398 " --> pdb=" O ARG A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1420 through 1426 removed outlier: 3.675A pdb=" N ASP A1426 " --> pdb=" O LYS A1422 " (cutoff:3.500A) Processing helix chain 'A' and resid 1464 through 1477 removed outlier: 3.563A pdb=" N GLY A1469 " --> pdb=" O GLU A1465 " (cutoff:3.500A) Processing helix chain 'A' and resid 1488 through 1492 Processing helix chain 'A' and resid 1518 through 1534 removed outlier: 3.576A pdb=" N TRP A1522 " --> pdb=" O GLU A1518 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE A1527 " --> pdb=" O LEU A1523 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA A1528 " --> pdb=" O GLY A1524 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS A1529 " --> pdb=" O LYS A1525 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A1530 " --> pdb=" O GLY A1526 " (cutoff:3.500A) Processing helix chain 'A' and resid 1538 through 1548 removed outlier: 3.583A pdb=" N LYS A1545 " --> pdb=" O ILE A1541A" (cutoff:3.500A) Processing helix chain 'A' and resid 1588 through 1593 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 3.501A pdb=" N ILE A 204 " --> pdb=" O THR A 3 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 8 through 11 Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 55 removed outlier: 3.965A pdb=" N TRP A 42 " --> pdb=" O THR A 18 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 403 through 404 removed outlier: 4.118A pdb=" N ASP A 581 " --> pdb=" O GLU A 403 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 527 through 531 removed outlier: 7.615A pdb=" N CYS A 407 " --> pdb=" O ALA A 575 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ALA A 575 " --> pdb=" O CYS A 407 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 441 through 442 removed outlier: 3.976A pdb=" N ALA A 488 " --> pdb=" O LEU A 442 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 497 through 504 removed outlier: 3.597A pdb=" N ARG A 503 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA A 515 " --> pdb=" O ARG A 503 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 659 through 661 removed outlier: 7.541A pdb=" N CYS A 672 " --> pdb=" O PHE A 730 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE A 730 " --> pdb=" O CYS A 672 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 659 through 661 removed outlier: 7.541A pdb=" N CYS A 672 " --> pdb=" O PHE A 730 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE A 730 " --> pdb=" O CYS A 672 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ASN A 629 " --> pdb=" O ILE A 822 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ILE A 822 " --> pdb=" O ASN A 629 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N SER A 631 " --> pdb=" O LEU A 820 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LEU A 820 " --> pdb=" O SER A 631 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLU A 633 " --> pdb=" O LYS A 818 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 655 through 656 Processing sheet with id=AB2, first strand: chain 'A' and resid 861 through 862 Processing sheet with id=AB3, first strand: chain 'A' and resid 865 through 868 Processing sheet with id=AB4, first strand: chain 'A' and resid 1357 through 1358 Processing sheet with id=AB5, first strand: chain 'A' and resid 1357 through 1358 removed outlier: 3.622A pdb=" N PHE A1460 " --> pdb=" O GLY A 893 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY A 893 " --> pdb=" O PHE A1460 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU A 891 " --> pdb=" O ASN A1462 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N THR A 892 " --> pdb=" O LEU A1505 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU A1505 " --> pdb=" O THR A 892 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LYS A 894 " --> pdb=" O VAL A1503 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N VAL A1503 " --> pdb=" O LYS A 894 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ARG A 896 " --> pdb=" O GLU A1501 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A 900 " --> pdb=" O GLU A1497 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU A1497 " --> pdb=" O ILE A 900 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 932 through 933 removed outlier: 6.643A pdb=" N LYS A 932 " --> pdb=" O THR A1444 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 976 through 978 Processing sheet with id=AB8, first strand: chain 'A' and resid 1227 through 1228 removed outlier: 3.812A pdb=" N TYR A1228 " --> pdb=" O ILE A1002 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A1002 " --> pdb=" O TYR A1228 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N HIS A1001 " --> pdb=" O THR A 996 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N THR A 996 " --> pdb=" O HIS A1001 " (cutoff:3.500A) 301 hydrogen bonds defined for protein. 828 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 2.32 Time building geometry restraints manager: 1.20 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: 3326 1.34 - 1.46: 2095 1.46 - 1.58: 5514 1.58 - 1.70: 77 1.70 - 1.82: 70 Bond restraints: 11082 Sorted by residual: bond pdb=" N ARG A 147 " pdb=" CA ARG A 147 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.00e-02 1.00e+04 1.10e+01 bond pdb=" N ILE A 148 " pdb=" CA ILE A 148 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.84e+00 bond pdb=" C THR A1595 " pdb=" N PRO A1596 " ideal model delta sigma weight residual 1.330 1.362 -0.032 1.22e-02 6.72e+03 7.08e+00 bond pdb=" N LYS A1567 " pdb=" CA LYS A1567 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.21e-02 6.83e+03 7.05e+00 bond pdb=" C ILE A1230 " pdb=" N PRO A1231 " ideal model delta sigma weight residual 1.328 1.354 -0.026 1.25e-02 6.40e+03 4.26e+00 ... (remaining 11077 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 14719 1.79 - 3.58: 296 3.58 - 5.36: 91 5.36 - 7.15: 6 7.15 - 8.94: 3 Bond angle restraints: 15115 Sorted by residual: angle pdb=" CA ILE A 148 " pdb=" C ILE A 148 " pdb=" O ILE A 148 " ideal model delta sigma weight residual 120.78 115.43 5.35 1.25e+00 6.40e-01 1.83e+01 angle pdb=" C4' U R 1 " pdb=" C3' U R 1 " pdb=" O3' U R 1 " ideal model delta sigma weight residual 113.00 104.93 8.07 2.00e+00 2.50e-01 1.63e+01 angle pdb=" C1' G R 10 " pdb=" N9 G R 10 " pdb=" C4 G R 10 " ideal model delta sigma weight residual 126.50 131.39 -4.89 1.30e+00 5.92e-01 1.41e+01 angle pdb=" O3' U R 0 " pdb=" C3' U R 0 " pdb=" C2' U R 0 " ideal model delta sigma weight residual 113.70 107.86 5.84 1.60e+00 3.91e-01 1.33e+01 angle pdb=" CA LYS A1567 " pdb=" C LYS A1567 " pdb=" O LYS A1567 " ideal model delta sigma weight residual 120.55 116.80 3.75 1.06e+00 8.90e-01 1.25e+01 ... (remaining 15110 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.80: 6430 29.80 - 59.61: 299 59.61 - 89.41: 42 89.41 - 119.22: 5 119.22 - 149.02: 1 Dihedral angle restraints: 6777 sinusoidal: 3227 harmonic: 3550 Sorted by residual: dihedral pdb=" O4' U R 0 " pdb=" C1' U R 0 " pdb=" N1 U R 0 " pdb=" C2 U R 0 " ideal model delta sinusoidal sigma weight residual 200.00 50.98 149.02 1 1.50e+01 4.44e-03 7.92e+01 dihedral pdb=" O4' U R 0 " pdb=" C2' U R 0 " pdb=" C1' U R 0 " pdb=" C3' U R 0 " ideal model delta sinusoidal sigma weight residual 25.00 -1.70 26.70 1 8.00e+00 1.56e-02 1.60e+01 dihedral pdb=" C4' U R 0 " pdb=" O4' U R 0 " pdb=" C1' U R 0 " pdb=" C2' U R 0 " ideal model delta sinusoidal sigma weight residual 3.00 -23.54 26.54 1 8.00e+00 1.56e-02 1.58e+01 ... (remaining 6774 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1361 0.053 - 0.106: 199 0.106 - 0.158: 63 0.158 - 0.211: 3 0.211 - 0.264: 1 Chirality restraints: 1627 Sorted by residual: chirality pdb=" P G R 2 " pdb=" OP1 G R 2 " pdb=" OP2 G R 2 " pdb=" O5' G R 2 " both_signs ideal model delta sigma weight residual True 2.41 -2.67 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" C3' U R 0 " pdb=" C4' U R 0 " pdb=" O3' U R 0 " pdb=" C2' U R 0 " both_signs ideal model delta sigma weight residual False -2.48 -2.68 0.20 2.00e-01 2.50e+01 9.81e-01 chirality pdb=" CB ILE A 148 " pdb=" CA ILE A 148 " pdb=" CG1 ILE A 148 " pdb=" CG2 ILE A 148 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.46e-01 ... (remaining 1624 not shown) Planarity restraints: 1821 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A1376 " -0.073 5.00e-02 4.00e+02 1.11e-01 1.98e+01 pdb=" N PRO A1377 " 0.192 5.00e-02 4.00e+02 pdb=" CA PRO A1377 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO A1377 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A1595 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.33e+00 pdb=" C THR A1595 " -0.032 2.00e-02 2.50e+03 pdb=" O THR A1595 " 0.011 2.00e-02 2.50e+03 pdb=" N PRO A1596 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 147 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" C ARG A 147 " 0.028 2.00e-02 2.50e+03 pdb=" O ARG A 147 " -0.010 2.00e-02 2.50e+03 pdb=" N ILE A 148 " -0.010 2.00e-02 2.50e+03 ... (remaining 1818 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1594 2.76 - 3.30: 9962 3.30 - 3.83: 16569 3.83 - 4.37: 19374 4.37 - 4.90: 33200 Nonbonded interactions: 80699 Sorted by model distance: nonbonded pdb=" O PHE A 417 " pdb=" OG SER A 560 " model vdw 2.226 3.040 nonbonded pdb=" O ALA A1449 " pdb=" ND2 ASN A1452 " model vdw 2.244 3.120 nonbonded pdb=" O GLN A 21 " pdb=" NH1 ARG A 26 " model vdw 2.251 3.120 nonbonded pdb=" O GLY A 555 " pdb=" NH1 ARG A 569 " model vdw 2.259 3.120 nonbonded pdb=" O GLU A1437 " pdb=" ND2 ASN A1442 " model vdw 2.265 3.120 ... (remaining 80694 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.260 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 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 : 0.004 0.037 11097 Z= 0.174 Angle : 0.694 12.274 15130 Z= 0.396 Chirality : 0.044 0.264 1627 Planarity : 0.005 0.111 1821 Dihedral : 16.396 149.022 4487 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.24), residues: 1215 helix: 0.85 (0.31), residues: 314 sheet: -0.17 (0.39), residues: 158 loop : -1.53 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A1535 TYR 0.017 0.001 TYR A 122 PHE 0.010 0.001 PHE A 187 TRP 0.010 0.001 TRP A 597 HIS 0.006 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 (11082) covalent geometry : angle 0.68067 / 0.40 (15115) hydrogen bonds : bond 0.21552 / 21.26 ( 293) hydrogen bonds : angle 7.83555 / 9.87 ( 828) metal coordination : bond 0.00462 / 0.40 ( 15) metal coordination : angle 4.35847 / 7.22 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.403 Fit side-chains REVERT: A 187 PHE cc_start: 0.7743 (p90) cc_final: 0.7522 (p90) REVERT: A 1563 MET cc_start: 0.5705 (pmm) cc_final: 0.5466 (ptp) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.0929 time to fit residues: 14.3243 Evaluate side-chains 71 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.0470 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 overall best weight: 0.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.135330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.108779 restraints weight = 21831.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.111848 restraints weight = 12521.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.113860 restraints weight = 8786.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.115180 restraints weight = 7009.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.115900 restraints weight = 6032.619| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11097 Z= 0.111 Angle : 0.554 10.596 15130 Z= 0.278 Chirality : 0.040 0.148 1627 Planarity : 0.005 0.081 1821 Dihedral : 14.965 149.401 1960 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.47 % Allowed : 6.48 % Favored : 93.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.24), residues: 1215 helix: 1.03 (0.31), residues: 317 sheet: -0.12 (0.39), residues: 163 loop : -1.44 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 349 TYR 0.017 0.001 TYR A 122 PHE 0.027 0.001 PHE A 916 TRP 0.009 0.001 TRP A 597 HIS 0.010 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (11082) covalent geometry : angle 0.54004 / 0.28 (15115) hydrogen bonds : bond 0.04196 / 4.25 ( 293) hydrogen bonds : angle 5.89503 / 7.51 ( 828) metal coordination : bond 0.00435 / 0.35 ( 15) metal coordination : angle 3.98593 / 6.79 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.378 Fit side-chains REVERT: A 1600 TRP cc_start: 0.7526 (p-90) cc_final: 0.7314 (p-90) outliers start: 5 outliers final: 3 residues processed: 78 average time/residue: 0.0860 time to fit residues: 10.2943 Evaluate side-chains 72 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 671 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 9 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 86 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 64 optimal weight: 0.0170 chunk 7 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 56 optimal weight: 0.0670 chunk 1 optimal weight: 20.0000 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.137420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.110541 restraints weight = 21966.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.113652 restraints weight = 12628.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.115731 restraints weight = 8859.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.117032 restraints weight = 7014.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.117784 restraints weight = 6035.532| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11097 Z= 0.090 Angle : 0.499 12.464 15130 Z= 0.250 Chirality : 0.038 0.147 1627 Planarity : 0.004 0.058 1821 Dihedral : 14.900 149.047 1960 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.66 % Allowed : 7.14 % Favored : 92.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.24), residues: 1215 helix: 1.19 (0.32), residues: 317 sheet: -0.17 (0.38), residues: 172 loop : -1.41 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 349 TYR 0.012 0.001 TYR A 122 PHE 0.022 0.001 PHE A 187 TRP 0.009 0.001 TRP A 597 HIS 0.004 0.000 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00188 / 0.09 (11082) covalent geometry : angle 0.49044 / 0.25 (15115) hydrogen bonds : bond 0.03708 / 3.70 ( 293) hydrogen bonds : angle 5.39945 / 6.85 ( 828) metal coordination : bond 0.00383 / 0.29 ( 15) metal coordination : angle 2.96369 / 4.93 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 349 ARG cc_start: 0.6836 (ptm160) cc_final: 0.6631 (ptm160) REVERT: A 355 LEU cc_start: 0.7801 (mt) cc_final: 0.7540 (tt) REVERT: A 1600 TRP cc_start: 0.7586 (p-90) cc_final: 0.7243 (p-90) outliers start: 7 outliers final: 6 residues processed: 79 average time/residue: 0.0933 time to fit residues: 11.0934 Evaluate side-chains 74 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 1445 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 57 optimal weight: 0.0970 chunk 42 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 801 ASN A1438 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.130662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.103361 restraints weight = 22359.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.106326 restraints weight = 13030.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.108244 restraints weight = 9250.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.109538 restraints weight = 7447.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.110295 restraints weight = 6446.848| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11097 Z= 0.148 Angle : 0.534 9.461 15130 Z= 0.270 Chirality : 0.040 0.154 1627 Planarity : 0.004 0.055 1821 Dihedral : 15.050 148.984 1960 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.22 % Allowed : 8.08 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.24), residues: 1215 helix: 1.07 (0.32), residues: 319 sheet: -0.43 (0.37), residues: 189 loop : -1.42 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 196 TYR 0.009 0.001 TYR A 122 PHE 0.021 0.002 PHE A 11 TRP 0.007 0.001 TRP A 597 HIS 0.004 0.001 HIS A1279 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (11082) covalent geometry : angle 0.52244 / 0.27 (15115) hydrogen bonds : bond 0.03902 / 3.97 ( 293) hydrogen bonds : angle 5.18941 / 6.52 ( 828) metal coordination : bond 0.00571 / 0.49 ( 15) metal coordination : angle 3.54922 / 5.87 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 VAL cc_start: 0.7963 (t) cc_final: 0.7585 (m) REVERT: A 349 ARG cc_start: 0.6967 (ptm160) cc_final: 0.6753 (ptm160) REVERT: A 355 LEU cc_start: 0.7795 (mt) cc_final: 0.7529 (tt) REVERT: A 1600 TRP cc_start: 0.7748 (p-90) cc_final: 0.7264 (p-90) outliers start: 13 outliers final: 11 residues processed: 80 average time/residue: 0.0939 time to fit residues: 11.4133 Evaluate side-chains 74 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1445 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 19 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 74 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 15 optimal weight: 0.0770 chunk 64 optimal weight: 5.9990 overall best weight: 3.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 505 ASN A 626 HIS A 963 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.127180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.100082 restraints weight = 22391.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.102868 restraints weight = 13278.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.104714 restraints weight = 9545.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.105882 restraints weight = 7755.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.106670 restraints weight = 6773.770| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11097 Z= 0.197 Angle : 0.597 8.822 15130 Z= 0.304 Chirality : 0.042 0.138 1627 Planarity : 0.005 0.039 1821 Dihedral : 15.394 148.219 1960 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.50 % Allowed : 9.58 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.24), residues: 1215 helix: 0.87 (0.31), residues: 318 sheet: -0.54 (0.38), residues: 169 loop : -1.64 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 890 TYR 0.014 0.002 TYR A1283 PHE 0.021 0.002 PHE A 187 TRP 0.010 0.001 TRP A1512 HIS 0.005 0.002 HIS A 691 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.20 (11082) covalent geometry : angle 0.58659 / 0.30 (15115) hydrogen bonds : bond 0.04439 / 4.55 ( 293) hydrogen bonds : angle 5.25663 / 6.62 ( 828) metal coordination : bond 0.00710 / 0.67 ( 15) metal coordination : angle 3.58396 / 5.78 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 VAL cc_start: 0.7982 (t) cc_final: 0.7632 (m) REVERT: A 349 ARG cc_start: 0.6982 (ptm160) cc_final: 0.6780 (ptm160) outliers start: 16 outliers final: 11 residues processed: 77 average time/residue: 0.0839 time to fit residues: 9.9601 Evaluate side-chains 74 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 672 CYS Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 798 ASP Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1445 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 83 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 81 optimal weight: 0.0470 chunk 14 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 113 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 overall best weight: 1.5882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.128610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.101606 restraints weight = 22097.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.104481 restraints weight = 13010.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.106368 restraints weight = 9280.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.107544 restraints weight = 7493.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.108265 restraints weight = 6544.210| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11097 Z= 0.122 Angle : 0.526 11.662 15130 Z= 0.264 Chirality : 0.039 0.132 1627 Planarity : 0.004 0.040 1821 Dihedral : 15.322 149.908 1960 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.88 % Allowed : 10.42 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.24), residues: 1215 helix: 1.01 (0.32), residues: 318 sheet: -0.51 (0.38), residues: 174 loop : -1.54 (0.22), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 890 TYR 0.012 0.001 TYR A1283 PHE 0.018 0.001 PHE A 187 TRP 0.008 0.001 TRP A1600 HIS 0.004 0.001 HIS A1279 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (11082) covalent geometry : angle 0.51754 / 0.26 (15115) hydrogen bonds : bond 0.03607 / 3.68 ( 293) hydrogen bonds : angle 5.08312 / 6.43 ( 828) metal coordination : bond 0.00480 / 0.39 ( 15) metal coordination : angle 2.94322 / 4.92 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.6935 (ptm160) cc_final: 0.6728 (ptm160) outliers start: 20 outliers final: 10 residues processed: 82 average time/residue: 0.0868 time to fit residues: 10.9711 Evaluate side-chains 77 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1290 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 102 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 66 optimal weight: 0.0470 chunk 25 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.3980 chunk 112 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.128826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.101882 restraints weight = 21976.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.104744 restraints weight = 12987.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.106630 restraints weight = 9302.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.107822 restraints weight = 7498.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.108526 restraints weight = 6542.874| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11097 Z= 0.124 Angle : 0.529 9.286 15130 Z= 0.266 Chirality : 0.039 0.140 1627 Planarity : 0.004 0.041 1821 Dihedral : 15.318 150.618 1960 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 1.60 % Allowed : 11.27 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.24), residues: 1215 helix: 0.94 (0.31), residues: 324 sheet: -0.50 (0.38), residues: 174 loop : -1.54 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 890 TYR 0.011 0.001 TYR A1283 PHE 0.018 0.001 PHE A 197 TRP 0.006 0.001 TRP A1600 HIS 0.007 0.001 HIS A1483 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (11082) covalent geometry : angle 0.52119 / 0.27 (15115) hydrogen bonds : bond 0.03563 / 3.64 ( 293) hydrogen bonds : angle 5.04013 / 6.32 ( 828) metal coordination : bond 0.00494 / 0.43 ( 15) metal coordination : angle 2.87320 / 4.73 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 60 LEU cc_start: 0.3803 (OUTLIER) cc_final: 0.3496 (tt) REVERT: A 232 LEU cc_start: 0.7240 (mt) cc_final: 0.6909 (mp) REVERT: A 349 ARG cc_start: 0.6920 (ptm160) cc_final: 0.6719 (ptm160) REVERT: A 1541 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8230 (tp) outliers start: 17 outliers final: 14 residues processed: 78 average time/residue: 0.0844 time to fit residues: 10.0904 Evaluate side-chains 82 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 672 CYS Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1541 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 67 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.128951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.102019 restraints weight = 22041.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.104890 restraints weight = 12976.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.106785 restraints weight = 9281.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.107991 restraints weight = 7482.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.108706 restraints weight = 6517.240| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 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 0.031 11097 Z= 0.119 Angle : 0.519 8.815 15130 Z= 0.262 Chirality : 0.039 0.130 1627 Planarity : 0.004 0.041 1821 Dihedral : 15.311 151.844 1960 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.60 % Allowed : 11.55 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.24), residues: 1215 helix: 0.97 (0.31), residues: 324 sheet: -0.48 (0.38), residues: 174 loop : -1.54 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 890 TYR 0.010 0.001 TYR A1283 PHE 0.019 0.001 PHE A 187 TRP 0.006 0.001 TRP A1600 HIS 0.011 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (11082) covalent geometry : angle 0.51173 / 0.26 (15115) hydrogen bonds : bond 0.03427 / 3.51 ( 293) hydrogen bonds : angle 4.96681 / 6.23 ( 828) metal coordination : bond 0.00479 / 0.40 ( 15) metal coordination : angle 2.76659 / 4.55 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 60 LEU cc_start: 0.3750 (OUTLIER) cc_final: 0.3456 (tt) REVERT: A 232 LEU cc_start: 0.7434 (mt) cc_final: 0.7045 (mp) REVERT: A 1541 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8229 (tp) outliers start: 17 outliers final: 12 residues processed: 81 average time/residue: 0.0736 time to fit residues: 9.2980 Evaluate side-chains 82 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 672 CYS Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1541 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 102 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 0.0050 chunk 101 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.128570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.101653 restraints weight = 21940.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.104495 restraints weight = 12987.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.106371 restraints weight = 9306.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.107556 restraints weight = 7519.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.108099 restraints weight = 6557.177| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11097 Z= 0.131 Angle : 0.531 8.258 15130 Z= 0.268 Chirality : 0.039 0.128 1627 Planarity : 0.004 0.041 1821 Dihedral : 15.343 152.396 1960 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 1.78 % Allowed : 11.64 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.24), residues: 1215 helix: 0.96 (0.31), residues: 324 sheet: -0.49 (0.38), residues: 174 loop : -1.57 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 890 TYR 0.010 0.001 TYR A 122 PHE 0.026 0.002 PHE A 33 TRP 0.005 0.001 TRP A 977 HIS 0.004 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (11082) covalent geometry : angle 0.52391 / 0.27 (15115) hydrogen bonds : bond 0.03533 / 3.62 ( 293) hydrogen bonds : angle 4.91591 / 6.18 ( 828) metal coordination : bond 0.00496 / 0.42 ( 15) metal coordination : angle 2.76759 / 4.55 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 60 LEU cc_start: 0.3853 (OUTLIER) cc_final: 0.3555 (tt) REVERT: A 232 LEU cc_start: 0.7457 (mt) cc_final: 0.7041 (mp) REVERT: A 1487 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.7381 (tpt) REVERT: A 1541 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8244 (tp) outliers start: 19 outliers final: 14 residues processed: 78 average time/residue: 0.0757 time to fit residues: 9.1805 Evaluate side-chains 85 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 672 CYS Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 914 ASP Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1487 MET Chi-restraints excluded: chain A residue 1541 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 61 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 93 optimal weight: 0.0980 chunk 69 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 80 optimal weight: 0.0470 chunk 42 optimal weight: 8.9990 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.132413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.106340 restraints weight = 21648.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.109275 restraints weight = 12820.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.111176 restraints weight = 9165.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.112340 restraints weight = 7395.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.113155 restraints weight = 6465.092| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11097 Z= 0.100 Angle : 0.514 8.268 15130 Z= 0.259 Chirality : 0.038 0.136 1627 Planarity : 0.004 0.042 1821 Dihedral : 15.286 152.731 1960 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.69 % Allowed : 11.64 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.24), residues: 1215 helix: 1.04 (0.31), residues: 324 sheet: -0.40 (0.38), residues: 174 loop : -1.52 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 890 TYR 0.016 0.001 TYR A1283 PHE 0.020 0.001 PHE A 33 TRP 0.007 0.001 TRP A1600 HIS 0.004 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (11082) covalent geometry : angle 0.50808 / 0.26 (15115) hydrogen bonds : bond 0.03143 / 3.20 ( 293) hydrogen bonds : angle 4.84750 / 6.11 ( 828) metal coordination : bond 0.00553 / 0.43 ( 15) metal coordination : angle 2.60399 / 4.33 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 60 LEU cc_start: 0.3739 (OUTLIER) cc_final: 0.3450 (tt) REVERT: A 232 LEU cc_start: 0.7405 (mt) cc_final: 0.7041 (mp) REVERT: A 1487 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.7496 (tpt) REVERT: A 1541 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8177 (tp) outliers start: 18 outliers final: 12 residues processed: 81 average time/residue: 0.0757 time to fit residues: 9.6402 Evaluate side-chains 85 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 672 CYS Chi-restraints excluded: chain A residue 687 VAL Chi-restraints excluded: chain A residue 914 ASP Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1487 MET Chi-restraints excluded: chain A residue 1541 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.132855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.106852 restraints weight = 21694.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.109790 restraints weight = 12826.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.111696 restraints weight = 9171.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.112846 restraints weight = 7393.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.113656 restraints weight = 6461.733| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11097 Z= 0.096 Angle : 0.523 10.556 15130 Z= 0.260 Chirality : 0.038 0.305 1627 Planarity : 0.004 0.041 1821 Dihedral : 15.261 153.342 1960 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.41 % Allowed : 12.11 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.24), residues: 1215 helix: 1.10 (0.31), residues: 323 sheet: -0.37 (0.38), residues: 174 loop : -1.49 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 890 TYR 0.011 0.001 TYR A 591 PHE 0.030 0.001 PHE A1277 TRP 0.006 0.001 TRP A1549 HIS 0.004 0.001 HIS A1483 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (11082) covalent geometry : angle 0.51707 / 0.26 (15115) hydrogen bonds : bond 0.03099 / 3.15 ( 293) hydrogen bonds : angle 4.79540 / 6.05 ( 828) metal coordination : bond 0.00536 / 0.43 ( 15) metal coordination : angle 2.52661 / 4.17 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1661.97 seconds wall clock time: 29 minutes 29.76 seconds (1769.76 seconds total)