Starting phenix.real_space_refine on Thu Jul 2 23:13:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wmi_37653/07_2026/8wmi_37653.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wmi_37653/07_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_37653/07_2026/8wmi_37653.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wmi_37653/07_2026/8wmi_37653.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wmi_37653/07_2026/8wmi_37653.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wmi_37653/07_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-dev-6108/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: 2.54, per 1000 atoms: 0.24 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: 0.86 Conformation dependent library (CDL) restraints added in 354.3 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: 1.27 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: 1.99 Time building geometry restraints manager: 1.14 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: 14773 1.79 - 3.58: 240 3.58 - 5.36: 93 5.36 - 7.15: 6 7.15 - 8.94: 3 Bond angle restraints: 15115 Sorted by residual: 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 1.50e+00 4.44e-01 2.90e+01 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=" 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 1.50e+00 4.44e-01 1.52e+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=" 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: 1399 0.053 - 0.106: 164 0.106 - 0.158: 58 0.158 - 0.211: 3 0.211 - 0.264: 3 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=" C2' U R 0 " pdb=" C3' U R 0 " pdb=" O2' U R 0 " pdb=" C1' U R 0 " both_signs ideal model delta sigma weight residual False -2.75 -2.50 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" C2' U R 1 " pdb=" C3' U R 1 " pdb=" O2' U R 1 " pdb=" C1' U R 1 " both_signs ideal model delta sigma weight residual False -2.75 -2.54 -0.21 2.00e-01 2.50e+01 1.14e+00 ... (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: 1.680 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.250 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.590 ------------------------------------------------------------------------------- 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 : 0.003 0.037 11097 Z= 0.170 Angle : 0.677 12.274 15130 Z= 0.368 Chirality : 0.042 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 0.00349 / 0.17 (11082) covalent geometry : angle 0.66336 / 0.37 (15115) hydrogen bonds : bond 0.21552 / 18.70 ( 293) hydrogen bonds : angle 7.83555 / 9.36 ( 828) metal coordination : bond 0.00462 / 0.31 ( 15) metal coordination : angle 4.35847 / 7.13 ( 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 : 0.483 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: 0.0988 time to fit residues: 15.0834 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 : 0.423 ------------------------------------------------------------------------------- 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 = 0.4055 r_free = 0.4055 target = 0.135270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.108771 restraints weight = 21835.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.111850 restraints weight = 12504.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.113862 restraints weight = 8774.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.115135 restraints weight = 6983.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.115979 restraints weight = 6026.816| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11097 Z= 0.113 Angle : 0.546 10.679 15130 Z= 0.276 Chirality : 0.039 0.219 1627 Planarity : 0.005 0.083 1821 Dihedral : 15.046 147.180 1960 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.38 % Allowed : 6.48 % Favored : 93.15 % 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: -0.81 (0.24), residues: 1215 helix: 1.08 (0.31), residues: 317 sheet: -0.10 (0.39), residues: 163 loop : -1.44 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 196 TYR 0.015 0.001 TYR A 122 PHE 0.017 0.001 PHE A 916 TRP 0.009 0.001 TRP A 597 HIS 0.007 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (11082) covalent geometry : angle 0.53135 / 0.27 (15115) hydrogen bonds : bond 0.04503 / 3.96 ( 293) hydrogen bonds : angle 5.98718 / 7.25 ( 828) metal coordination : bond 0.00398 / 0.26 ( 15) metal coordination : angle 3.98917 / 6.72 ( 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 79 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.394 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 76 average time/residue: 0.0937 time to fit residues: 10.8936 Evaluate side-chains 70 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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: 3.9990 chunk 30 optimal weight: 0.0470 chunk 62 optimal weight: 0.0470 chunk 86 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 7 optimal weight: 0.3980 chunk 28 optimal weight: 9.9990 chunk 56 optimal weight: 0.0470 chunk 1 optimal weight: 10.0000 overall best weight: 0.3076 ------------------------------------------------------------------------------- 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 = 0.4075 r_free = 0.4075 target = 0.137680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.110698 restraints weight = 21882.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.113836 restraints weight = 12551.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.115870 restraints weight = 8786.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.117231 restraints weight = 6990.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.117983 restraints weight = 5999.764| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1223 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 : 0.495 10.684 15130 Z= 0.249 Chirality : 0.038 0.189 1627 Planarity : 0.004 0.061 1821 Dihedral : 14.937 146.492 1960 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.66 % Allowed : 7.23 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.74 (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 0.002 0.000 ARG A1535 TYR 0.013 0.001 TYR A 122 PHE 0.021 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 0.00186 / 0.09 (11082) covalent geometry : angle 0.48629 / 0.25 (15115) hydrogen bonds : bond 0.03653 / 3.23 ( 293) hydrogen bonds : angle 5.41953 / 6.54 ( 828) metal coordination : bond 0.00365 / 0.24 ( 15) metal coordination : angle 2.97227 / 4.91 ( 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 84 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: A 129 LEU cc_start: 0.7326 (pp) cc_final: 0.7054 (mt) REVERT: A 349 ARG cc_start: 0.6862 (ptm160) cc_final: 0.6630 (ptm160) REVERT: A 355 LEU cc_start: 0.7788 (mt) cc_final: 0.7528 (tt) REVERT: A 1600 TRP cc_start: 0.7552 (p-90) cc_final: 0.7236 (p-90) outliers start: 7 outliers final: 5 residues processed: 80 average time/residue: 0.0908 time to fit residues: 11.2252 Evaluate side-chains 75 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.0370 chunk 26 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 626 HIS A 801 ASN A1438 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.130096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.102747 restraints weight = 22420.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.105621 restraints weight = 13063.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.107604 restraints weight = 9333.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.108870 restraints weight = 7478.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.109651 restraints weight = 6485.303| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11097 Z= 0.167 Angle : 0.556 9.844 15130 Z= 0.282 Chirality : 0.040 0.196 1627 Planarity : 0.004 0.046 1821 Dihedral : 15.122 145.120 1960 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 1.13 % Allowed : 7.89 % Favored : 90.99 % 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: -0.90 (0.24), residues: 1215 helix: 1.04 (0.32), residues: 318 sheet: -0.45 (0.37), residues: 189 loop : -1.46 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 890 TYR 0.009 0.001 TYR A 122 PHE 0.019 0.002 PHE A 187 TRP 0.007 0.001 TRP A 977 HIS 0.004 0.001 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (11082) covalent geometry : angle 0.54323 / 0.28 (15115) hydrogen bonds : bond 0.04171 / 3.81 ( 293) hydrogen bonds : angle 5.22554 / 6.22 ( 828) metal coordination : bond 0.00611 / 0.41 ( 15) metal coordination : angle 3.73302 / 6.05 ( 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 83 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 11 residues processed: 79 average time/residue: 0.1009 time to fit residues: 11.8623 Evaluate side-chains 75 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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: 6.9990 chunk 83 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 99 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 505 ASN A 741 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 = 0.3918 r_free = 0.3918 target = 0.126043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.098950 restraints weight = 22499.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.101709 restraints weight = 13320.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.103524 restraints weight = 9614.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.104688 restraints weight = 7807.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.105454 restraints weight = 6832.642| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11097 Z= 0.226 Angle : 0.629 8.643 15130 Z= 0.323 Chirality : 0.043 0.209 1627 Planarity : 0.005 0.084 1821 Dihedral : 15.594 143.869 1960 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % 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: -1.33 (0.23), residues: 1215 helix: 0.67 (0.31), residues: 317 sheet: -0.62 (0.38), residues: 169 loop : -1.73 (0.21), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 890 TYR 0.015 0.002 TYR A 190 PHE 0.023 0.002 PHE A 187 TRP 0.011 0.001 TRP A1600 HIS 0.006 0.002 HIS A1279 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.23 (11082) covalent geometry : angle 0.61732 / 0.32 (15115) hydrogen bonds : bond 0.04748 / 4.43 ( 293) hydrogen bonds : angle 5.39570 / 6.44 ( 828) metal coordination : bond 0.00699 / 0.51 ( 15) metal coordination : angle 3.81783 / 5.93 ( 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 84 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 232 LEU cc_start: 0.7195 (mt) cc_final: 0.6842 (mp) outliers start: 16 outliers final: 12 residues processed: 80 average time/residue: 0.0980 time to fit residues: 11.8158 Evaluate side-chains 75 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 26 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 113 optimal weight: 0.9980 chunk 7 optimal weight: 0.3980 chunk 46 optimal weight: 7.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 = 0.3938 r_free = 0.3938 target = 0.127503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.100560 restraints weight = 22180.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.103365 restraints weight = 13108.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.105209 restraints weight = 9413.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.106366 restraints weight = 7620.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.107143 restraints weight = 6659.961| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11097 Z= 0.147 Angle : 0.552 11.191 15130 Z= 0.280 Chirality : 0.040 0.197 1627 Planarity : 0.004 0.041 1821 Dihedral : 15.496 145.070 1960 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.88 % Allowed : 10.05 % Favored : 88.08 % 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: -1.17 (0.24), residues: 1215 helix: 0.85 (0.31), residues: 318 sheet: -0.49 (0.38), residues: 166 loop : -1.67 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 196 TYR 0.010 0.001 TYR A 122 PHE 0.019 0.002 PHE A 187 TRP 0.022 0.001 TRP A1600 HIS 0.009 0.001 HIS A1483 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (11082) covalent geometry : angle 0.54338 / 0.28 (15115) hydrogen bonds : bond 0.03911 / 3.62 ( 293) hydrogen bonds : angle 5.20294 / 6.27 ( 828) metal coordination : bond 0.00531 / 0.36 ( 15) metal coordination : angle 3.16458 / 5.13 ( 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 90 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 232 LEU cc_start: 0.7221 (mt) cc_final: 0.6870 (mp) REVERT: A 1541 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8260 (tp) outliers start: 20 outliers final: 13 residues processed: 82 average time/residue: 0.0853 time to fit residues: 10.8330 Evaluate side-chains 78 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 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 1274 LEU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1445 VAL Chi-restraints excluded: chain A residue 1541 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 102 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 58 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 124 optimal weight: 0.0470 chunk 103 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.129641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.102548 restraints weight = 21875.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.105503 restraints weight = 12734.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.107437 restraints weight = 9036.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.108661 restraints weight = 7254.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.109388 restraints weight = 6300.012| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11097 Z= 0.099 Angle : 0.527 15.911 15130 Z= 0.261 Chirality : 0.038 0.186 1627 Planarity : 0.004 0.043 1821 Dihedral : 15.358 145.838 1960 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.41 % Allowed : 11.64 % Favored : 86.95 % 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: -1.05 (0.24), residues: 1215 helix: 0.92 (0.31), residues: 324 sheet: -0.51 (0.38), residues: 174 loop : -1.58 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 890 TYR 0.011 0.001 TYR A 122 PHE 0.017 0.001 PHE A 187 TRP 0.023 0.001 TRP A1600 HIS 0.004 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (11082) covalent geometry : angle 0.52008 / 0.26 (15115) hydrogen bonds : bond 0.03319 / 3.07 ( 293) hydrogen bonds : angle 5.03526 / 6.08 ( 828) metal coordination : bond 0.00442 / 0.29 ( 15) metal coordination : angle 2.68418 / 4.37 ( 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 85 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.355 Fit side-chains REVERT: A 5 MET cc_start: 0.7196 (mtt) cc_final: 0.6988 (mtt) REVERT: A 60 LEU cc_start: 0.3698 (OUTLIER) cc_final: 0.3419 (tt) REVERT: A 232 LEU cc_start: 0.7200 (mt) cc_final: 0.6838 (mp) REVERT: A 605 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7458 (mp0) REVERT: A 1541 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8189 (tp) outliers start: 15 outliers final: 11 residues processed: 80 average time/residue: 0.0749 time to fit residues: 9.2804 Evaluate side-chains 80 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 96 ASP Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 626 HIS Chi-restraints excluded: chain A residue 671 VAL 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 1445 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: 3.9990 chunk 84 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 101 optimal weight: 0.3980 chunk 75 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 5 optimal weight: 0.4980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.129107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.102192 restraints weight = 22003.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.105051 restraints weight = 12946.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.106930 restraints weight = 9264.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.108146 restraints weight = 7476.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.108798 restraints weight = 6512.797| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11097 Z= 0.116 Angle : 0.542 15.514 15130 Z= 0.268 Chirality : 0.039 0.188 1627 Planarity : 0.004 0.042 1821 Dihedral : 15.310 146.228 1960 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.88 % Allowed : 11.17 % Favored : 86.95 % 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: -1.03 (0.24), residues: 1215 helix: 0.95 (0.31), residues: 324 sheet: -0.52 (0.38), residues: 174 loop : -1.57 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 890 TYR 0.010 0.001 TYR A 122 PHE 0.017 0.001 PHE A 187 TRP 0.021 0.001 TRP A1600 HIS 0.004 0.001 HIS A1279 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (11082) covalent geometry : angle 0.53525 / 0.27 (15115) hydrogen bonds : bond 0.03427 / 3.22 ( 293) hydrogen bonds : angle 4.92786 / 5.90 ( 828) metal coordination : bond 0.00458 / 0.31 ( 15) metal coordination : angle 2.67859 / 4.31 ( 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 93 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.336 Fit side-chains REVERT: A 60 LEU cc_start: 0.3588 (OUTLIER) cc_final: 0.3340 (tt) REVERT: A 232 LEU cc_start: 0.7289 (mt) cc_final: 0.6921 (mp) REVERT: A 605 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7451 (mp0) REVERT: A 1541 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8224 (tp) outliers start: 20 outliers final: 15 residues processed: 86 average time/residue: 0.0760 time to fit residues: 10.0283 Evaluate side-chains 87 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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 527 VAL Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 626 HIS 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 916 PHE 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 1445 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: 2.9990 chunk 64 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.3954 r_free = 0.3954 target = 0.128596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.101669 restraints weight = 21822.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.104515 restraints weight = 12919.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.106356 restraints weight = 9263.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.107557 restraints weight = 7491.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.108317 restraints weight = 6555.587| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2454 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= 0.128 Angle : 0.536 13.156 15130 Z= 0.270 Chirality : 0.039 0.187 1627 Planarity : 0.004 0.041 1821 Dihedral : 15.323 146.762 1960 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.97 % Allowed : 11.27 % Favored : 86.76 % 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: 0.98 (0.31), residues: 324 sheet: -0.43 (0.39), residues: 166 loop : -1.58 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 890 TYR 0.016 0.001 TYR A1283 PHE 0.028 0.002 PHE A 33 TRP 0.022 0.001 TRP A1600 HIS 0.004 0.001 HIS A1279 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (11082) covalent geometry : angle 0.52916 / 0.27 (15115) hydrogen bonds : bond 0.03545 / 3.32 ( 293) hydrogen bonds : angle 4.92604 / 5.87 ( 828) metal coordination : bond 0.00689 / 0.52 ( 15) metal coordination : angle 2.74531 / 4.37 ( 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 89 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 60 LEU cc_start: 0.3732 (OUTLIER) cc_final: 0.3444 (tt) REVERT: A 232 LEU cc_start: 0.7347 (mt) cc_final: 0.6912 (mp) REVERT: A 1541 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8164 (tp) outliers start: 21 outliers final: 15 residues processed: 82 average time/residue: 0.0863 time to fit residues: 10.8622 Evaluate side-chains 83 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.249 ------------------------------------------------------------------------------- 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 527 VAL Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 626 HIS 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 916 PHE Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1445 VAL 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: 5.9990 chunk 108 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 69 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 80 optimal weight: 0.0770 chunk 42 optimal weight: 8.9990 overall best weight: 1.5542 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.131005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.105050 restraints weight = 21609.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.107890 restraints weight = 12859.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.109766 restraints weight = 9228.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.110942 restraints weight = 7472.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.111710 restraints weight = 6537.013| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2509 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 : 0.545 12.814 15130 Z= 0.272 Chirality : 0.039 0.260 1627 Planarity : 0.004 0.042 1821 Dihedral : 15.299 146.807 1960 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.78 % Allowed : 11.55 % 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: -0.99 (0.24), residues: 1215 helix: 1.00 (0.31), residues: 324 sheet: -0.40 (0.39), residues: 166 loop : -1.58 (0.22), residues: 725 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 0.027 0.001 PHE A 915 TRP 0.021 0.001 TRP A1600 HIS 0.004 0.001 HIS A1279 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (11082) covalent geometry : angle 0.53821 / 0.27 (15115) hydrogen bonds : bond 0.03491 / 3.28 ( 293) hydrogen bonds : angle 4.91260 / 5.89 ( 828) metal coordination : bond 0.00545 / 0.40 ( 15) metal coordination : angle 2.69549 / 4.32 ( 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 86 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: A 60 LEU cc_start: 0.3945 (OUTLIER) cc_final: 0.3663 (tt) REVERT: A 232 LEU cc_start: 0.7319 (mt) cc_final: 0.6979 (mp) REVERT: A 1541 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.8133 (tp) outliers start: 19 outliers final: 15 residues processed: 80 average time/residue: 0.0891 time to fit residues: 11.0293 Evaluate side-chains 83 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 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 916 PHE 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 1445 VAL 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: 0.8980 chunk 31 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3976 r_free = 0.3976 target = 0.132274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.106399 restraints weight = 21634.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.109300 restraints weight = 12792.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.111221 restraints weight = 9136.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.112408 restraints weight = 7360.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.113067 restraints weight = 6431.152| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11097 Z= 0.100 Angle : 0.528 11.869 15130 Z= 0.264 Chirality : 0.039 0.209 1627 Planarity : 0.004 0.043 1821 Dihedral : 15.246 146.892 1960 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 1.50 % Allowed : 11.74 % Favored : 86.76 % 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: -0.95 (0.24), residues: 1215 helix: 1.05 (0.31), residues: 324 sheet: -0.45 (0.38), residues: 174 loop : -1.54 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 890 TYR 0.010 0.001 TYR A 122 PHE 0.016 0.001 PHE A 187 TRP 0.023 0.001 TRP A1600 HIS 0.004 0.001 HIS A1279 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (11082) covalent geometry : angle 0.52211 / 0.26 (15115) hydrogen bonds : bond 0.03182 / 3.00 ( 293) hydrogen bonds : angle 4.84506 / 5.81 ( 828) metal coordination : bond 0.00450 / 0.30 ( 15) metal coordination : angle 2.56283 / 4.12 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1717.96 seconds wall clock time: 30 minutes 32.90 seconds (1832.90 seconds total)