Starting phenix.real_space_refine on Tue May 13 18:09:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wmi_37653/05_2025/8wmi_37653.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wmi_37653/05_2025/8wmi_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wmi_37653/05_2025/8wmi_37653.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wmi_37653/05_2025/8wmi_37653.map" model { file = "/net/cci-nas-00/data/ceres_data/8wmi_37653/05_2025/8wmi_37653.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wmi_37653/05_2025/8wmi_37653.cif" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 'ARG:plan': 1, 'ASP: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: 6.45, per 1000 atoms: 0.60 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: 2.37 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 3.16 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: 3.94 Time building geometry restraints manager: 2.81 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=" 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 angle pdb=" O3' G R 2 " pdb=" C3' G R 2 " pdb=" C2' G R 2 " ideal model delta sigma weight residual 109.50 114.66 -5.16 1.50e+00 4.44e-01 1.19e+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: 1.330 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: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 29.520 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 34.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 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= 0.164 Angle : 0.677 12.274 15130 Z= 0.346 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 : 3.76 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (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 TRP 0.010 0.001 TRP A 597 HIS 0.006 0.001 HIS A 194 PHE 0.010 0.001 PHE A 187 TYR 0.017 0.001 TYR A 122 ARG 0.013 0.000 ARG A1535 Details of bonding type rmsd hydrogen bonds : bond 0.21552 ( 293) hydrogen bonds : angle 7.83555 ( 828) metal coordination : bond 0.00462 ( 15) metal coordination : angle 4.35847 ( 15) covalent geometry : bond 0.00349 (11082) covalent geometry : angle 0.66334 (15115) *********************** 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 : 1.162 Fit side-chains REVERT: A 187 PHE cc_start: 0.7743 (p90) cc_final: 0.7522 (p90) REVERT: A 1563 MET cc_start: 0.5706 (pmm) cc_final: 0.5466 (ptp) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.2254 time to fit residues: 34.2141 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 : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 114 optimal weight: 10.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.132991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.106053 restraints weight = 21846.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.109039 restraints weight = 12710.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.111022 restraints weight = 8997.619| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1261 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= 0.107 Angle : 0.521 9.782 15130 Z= 0.260 Chirality : 0.039 0.149 1627 Planarity : 0.004 0.083 1821 Dihedral : 15.000 143.420 1960 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.56 % Allowed : 6.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.24), residues: 1215 helix: 1.09 (0.32), residues: 319 sheet: -0.14 (0.39), residues: 177 loop : -1.41 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1600 HIS 0.003 0.001 HIS A1279 PHE 0.014 0.001 PHE A 916 TYR 0.012 0.001 TYR A 440 ARG 0.002 0.000 ARG A 196 Details of bonding type rmsd hydrogen bonds : bond 0.03782 ( 293) hydrogen bonds : angle 5.51323 ( 828) metal coordination : bond 0.00489 ( 15) metal coordination : angle 3.92077 ( 15) covalent geometry : bond 0.00237 (11082) covalent geometry : angle 0.50634 (15115) *********************** 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 80 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 PHE cc_start: 0.7772 (p90) cc_final: 0.7542 (p90) REVERT: A 355 LEU cc_start: 0.7794 (mt) cc_final: 0.7531 (tt) REVERT: A 1569 ASP cc_start: 0.4100 (t0) cc_final: 0.3849 (t70) outliers start: 6 outliers final: 4 residues processed: 76 average time/residue: 0.2111 time to fit residues: 24.6003 Evaluate side-chains 74 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 1.141 ------------------------------------------------------------------------------- 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 671 VAL Chi-restraints excluded: chain A residue 1445 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 67 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 108 optimal weight: 0.1980 chunk 75 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 0.4980 chunk 98 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 ASN A 626 HIS A 801 ASN A 963 ASN A1438 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.130584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.103329 restraints weight = 22270.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.106296 restraints weight = 12920.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.108300 restraints weight = 9136.446| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11097 Z= 0.121 Angle : 0.509 8.597 15130 Z= 0.255 Chirality : 0.039 0.152 1627 Planarity : 0.004 0.062 1821 Dihedral : 15.176 136.952 1960 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.85 % Allowed : 7.32 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.24), residues: 1215 helix: 1.13 (0.32), residues: 319 sheet: -0.33 (0.38), residues: 176 loop : -1.46 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1600 HIS 0.006 0.001 HIS A 194 PHE 0.014 0.001 PHE A1277 TYR 0.010 0.001 TYR A 122 ARG 0.002 0.000 ARG A 890 Details of bonding type rmsd hydrogen bonds : bond 0.03740 ( 293) hydrogen bonds : angle 5.06141 ( 828) metal coordination : bond 0.00537 ( 15) metal coordination : angle 3.27545 ( 15) covalent geometry : bond 0.00278 (11082) covalent geometry : angle 0.49828 (15115) *********************** 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 85 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 79 average time/residue: 0.2141 time to fit residues: 25.4283 Evaluate side-chains 77 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 1.053 ------------------------------------------------------------------------------- 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 361 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 687 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 112 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 3 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 98 optimal weight: 0.0670 chunk 99 optimal weight: 0.1980 chunk 94 optimal weight: 2.9990 overall best weight: 0.6522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.132929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.105855 restraints weight = 21839.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.108857 restraints weight = 12699.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.110835 restraints weight = 8994.229| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1977 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= 0.084 Angle : 0.471 8.474 15130 Z= 0.235 Chirality : 0.037 0.149 1627 Planarity : 0.004 0.048 1821 Dihedral : 14.978 134.206 1960 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.22 % Allowed : 8.54 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.24), residues: 1215 helix: 1.18 (0.31), residues: 320 sheet: -0.28 (0.37), residues: 183 loop : -1.37 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1600 HIS 0.003 0.000 HIS A1001 PHE 0.020 0.001 PHE A 915 TYR 0.009 0.001 TYR A 122 ARG 0.002 0.000 ARG A 196 Details of bonding type rmsd hydrogen bonds : bond 0.02924 ( 293) hydrogen bonds : angle 4.75714 ( 828) metal coordination : bond 0.00466 ( 15) metal coordination : angle 2.95189 ( 15) covalent geometry : bond 0.00187 (11082) covalent geometry : angle 0.46184 (15115) *********************** 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 94 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 PHE cc_start: 0.7780 (p90) cc_final: 0.7579 (p90) REVERT: A 1541 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8149 (tp) outliers start: 13 outliers final: 10 residues processed: 88 average time/residue: 0.2025 time to fit residues: 27.4851 Evaluate side-chains 83 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 1.136 ------------------------------------------------------------------------------- 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 96 ASP Chi-restraints excluded: chain A residue 361 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 687 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 43 optimal weight: 0.9980 chunk 105 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 125 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 741 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.126726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.099824 restraints weight = 22130.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.102616 restraints weight = 13078.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.104436 restraints weight = 9423.953| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11097 Z= 0.190 Angle : 0.589 7.883 15130 Z= 0.295 Chirality : 0.041 0.173 1627 Planarity : 0.004 0.037 1821 Dihedral : 15.459 133.166 1960 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 1.88 % Allowed : 9.30 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.24), residues: 1215 helix: 0.98 (0.32), residues: 319 sheet: -0.19 (0.39), residues: 166 loop : -1.55 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1600 HIS 0.005 0.001 HIS A1279 PHE 0.013 0.002 PHE A 197 TYR 0.012 0.002 TYR A1576 ARG 0.004 0.000 ARG A 890 Details of bonding type rmsd hydrogen bonds : bond 0.04219 ( 293) hydrogen bonds : angle 5.12203 ( 828) metal coordination : bond 0.00578 ( 15) metal coordination : angle 3.51530 ( 15) covalent geometry : bond 0.00440 (11082) covalent geometry : angle 0.57864 (15115) *********************** 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 97 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 1.298 Fit side-chains revert: symmetry clash REVERT: A 187 PHE cc_start: 0.7856 (p90) cc_final: 0.7561 (p90) REVERT: A 232 LEU cc_start: 0.7425 (mt) cc_final: 0.6932 (mp) REVERT: A 351 PHE cc_start: 0.7942 (t80) cc_final: 0.7266 (t80) REVERT: A 1305 MET cc_start: 0.6499 (ptt) cc_final: 0.6257 (ptt) REVERT: A 1541 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8217 (tp) outliers start: 20 outliers final: 14 residues processed: 84 average time/residue: 0.2151 time to fit residues: 27.8697 Evaluate side-chains 83 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 1.188 ------------------------------------------------------------------------------- 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 73 LEU Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 361 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 1541 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 18 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 84 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 10 optimal weight: 0.0970 chunk 58 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.132682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.106797 restraints weight = 21892.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.109712 restraints weight = 12860.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.111594 restraints weight = 9192.516| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2532 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= 0.097 Angle : 0.502 8.052 15130 Z= 0.248 Chirality : 0.038 0.155 1627 Planarity : 0.004 0.039 1821 Dihedral : 15.164 131.942 1960 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.97 % Allowed : 10.14 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.24), residues: 1215 helix: 1.02 (0.31), residues: 325 sheet: -0.21 (0.39), residues: 174 loop : -1.47 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1600 HIS 0.003 0.001 HIS A1279 PHE 0.026 0.001 PHE A 915 TYR 0.010 0.001 TYR A 122 ARG 0.002 0.000 ARG A 444 Details of bonding type rmsd hydrogen bonds : bond 0.03067 ( 293) hydrogen bonds : angle 4.76531 ( 828) metal coordination : bond 0.00424 ( 15) metal coordination : angle 2.63506 ( 15) covalent geometry : bond 0.00221 (11082) covalent geometry : angle 0.49551 (15115) *********************** 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 97 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.3700 (OUTLIER) cc_final: 0.3457 (tt) REVERT: A 187 PHE cc_start: 0.7771 (p90) cc_final: 0.7557 (p90) REVERT: A 351 PHE cc_start: 0.7740 (t80) cc_final: 0.7210 (t80) REVERT: A 1541 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8104 (tp) outliers start: 21 outliers final: 12 residues processed: 87 average time/residue: 0.2166 time to fit residues: 28.4871 Evaluate side-chains 85 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 1.143 ------------------------------------------------------------------------------- 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 361 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 1002 ILE Chi-restraints excluded: chain A residue 1290 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 26 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 0.0970 chunk 7 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 83 optimal weight: 0.6980 chunk 75 optimal weight: 0.0470 overall best weight: 0.9678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.131794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.104979 restraints weight = 22010.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.108174 restraints weight = 12428.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.110258 restraints weight = 8684.016| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2646 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= 0.096 Angle : 0.507 10.661 15130 Z= 0.247 Chirality : 0.037 0.157 1627 Planarity : 0.004 0.039 1821 Dihedral : 15.107 131.169 1960 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.69 % Allowed : 11.27 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.24), residues: 1215 helix: 1.13 (0.31), residues: 324 sheet: -0.29 (0.38), residues: 185 loop : -1.41 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1600 HIS 0.003 0.001 HIS A1279 PHE 0.011 0.001 PHE A 776 TYR 0.009 0.001 TYR A 122 ARG 0.004 0.000 ARG A1443 Details of bonding type rmsd hydrogen bonds : bond 0.03032 ( 293) hydrogen bonds : angle 4.61379 ( 828) metal coordination : bond 0.00421 ( 15) metal coordination : angle 2.58799 ( 15) covalent geometry : bond 0.00218 (11082) covalent geometry : angle 0.50115 (15115) *********************** 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 94 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 1.239 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6580 (mmp) cc_final: 0.6321 (mmp) REVERT: A 187 PHE cc_start: 0.7852 (p90) cc_final: 0.7585 (p90) REVERT: A 351 PHE cc_start: 0.7798 (t80) cc_final: 0.7256 (t80) REVERT: A 1541 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8076 (tp) outliers start: 18 outliers final: 14 residues processed: 85 average time/residue: 0.2033 time to fit residues: 26.7169 Evaluate side-chains 87 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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 361 LEU 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 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 50 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 81 optimal weight: 0.4980 chunk 3 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.129883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.103349 restraints weight = 21998.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.106382 restraints weight = 12672.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.108372 restraints weight = 8998.877| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11097 Z= 0.135 Angle : 0.535 10.365 15130 Z= 0.264 Chirality : 0.039 0.166 1627 Planarity : 0.004 0.038 1821 Dihedral : 15.222 128.793 1960 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.24), residues: 1215 helix: 1.10 (0.32), residues: 324 sheet: -0.16 (0.39), residues: 178 loop : -1.46 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 977 HIS 0.004 0.001 HIS A1279 PHE 0.030 0.001 PHE A 915 TYR 0.009 0.001 TYR A 122 ARG 0.004 0.000 ARG A1443 Details of bonding type rmsd hydrogen bonds : bond 0.03506 ( 293) hydrogen bonds : angle 4.79834 ( 828) metal coordination : bond 0.00458 ( 15) metal coordination : angle 2.65919 ( 15) covalent geometry : bond 0.00311 (11082) covalent geometry : angle 0.52867 (15115) *********************** 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 91 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 1.112 Fit side-chains revert: symmetry clash REVERT: A 60 LEU cc_start: 0.3807 (OUTLIER) cc_final: 0.3558 (tt) REVERT: A 351 PHE cc_start: 0.7808 (t80) cc_final: 0.7265 (t80) REVERT: A 1541 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8092 (tp) outliers start: 19 outliers final: 16 residues processed: 81 average time/residue: 0.2021 time to fit residues: 25.5244 Evaluate side-chains 88 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 1.223 ------------------------------------------------------------------------------- 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 73 LEU Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 361 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 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 100 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 90 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.127119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.100913 restraints weight = 22261.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.103796 restraints weight = 12928.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.105654 restraints weight = 9235.654| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11097 Z= 0.200 Angle : 0.614 10.267 15130 Z= 0.304 Chirality : 0.041 0.178 1627 Planarity : 0.004 0.040 1821 Dihedral : 15.497 127.574 1960 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 2.16 % Allowed : 11.46 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.24), residues: 1215 helix: 0.87 (0.31), residues: 324 sheet: -0.22 (0.39), residues: 183 loop : -1.64 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 977 HIS 0.005 0.001 HIS A1279 PHE 0.019 0.002 PHE A 187 TYR 0.010 0.002 TYR A 122 ARG 0.005 0.000 ARG A 890 Details of bonding type rmsd hydrogen bonds : bond 0.04274 ( 293) hydrogen bonds : angle 5.13513 ( 828) metal coordination : bond 0.00535 ( 15) metal coordination : angle 3.39289 ( 15) covalent geometry : bond 0.00465 (11082) covalent geometry : angle 0.60537 (15115) *********************** 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 92 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 1.155 Fit side-chains revert: symmetry clash REVERT: A 42 TRP cc_start: 0.7223 (t-100) cc_final: 0.5892 (t-100) REVERT: A 232 LEU cc_start: 0.7665 (mt) cc_final: 0.7185 (mt) REVERT: A 351 PHE cc_start: 0.7897 (t80) cc_final: 0.7287 (t80) REVERT: A 1541 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.8047 (tp) outliers start: 23 outliers final: 17 residues processed: 82 average time/residue: 0.2051 time to fit residues: 25.9700 Evaluate side-chains 85 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 502 THR 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 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 92 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 88 optimal weight: 0.6980 chunk 104 optimal weight: 0.0870 chunk 108 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 123 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.130199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.103837 restraints weight = 21987.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.106895 restraints weight = 12606.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.108884 restraints weight = 8916.408| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11097 Z= 0.114 Angle : 0.549 10.073 15130 Z= 0.270 Chirality : 0.038 0.164 1627 Planarity : 0.004 0.040 1821 Dihedral : 15.245 124.636 1960 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.50 % Allowed : 12.30 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.24), residues: 1215 helix: 1.04 (0.31), residues: 324 sheet: -0.21 (0.39), residues: 183 loop : -1.56 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1509 HIS 0.004 0.001 HIS A1483 PHE 0.031 0.001 PHE A 915 TYR 0.012 0.001 TYR A 122 ARG 0.004 0.000 ARG A1443 Details of bonding type rmsd hydrogen bonds : bond 0.03279 ( 293) hydrogen bonds : angle 4.82912 ( 828) metal coordination : bond 0.00463 ( 15) metal coordination : angle 2.68386 ( 15) covalent geometry : bond 0.00261 (11082) covalent geometry : angle 0.54319 (15115) ********************** 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: 16 poor density : 70 time to evaluate : 1.293 Fit side-chains revert: symmetry clash REVERT: A 42 TRP cc_start: 0.7004 (t-100) cc_final: 0.5742 (t-100) REVERT: A 351 PHE cc_start: 0.7856 (t80) cc_final: 0.7295 (t80) REVERT: A 1541 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8009 (tp) outliers start: 16 outliers final: 14 residues processed: 80 average time/residue: 0.2256 time to fit residues: 27.3637 Evaluate side-chains 81 residues out of total 1069 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 502 THR 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 1274 LEU Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1431 THR 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 64 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 93 optimal weight: 7.9990 chunk 111 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 122 optimal weight: 0.1980 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3920 r_free = 0.3920 target = 0.128423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.102351 restraints weight = 21887.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.105262 restraints weight = 12699.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.107137 restraints weight = 9059.816| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3254 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= 0.157 Angle : 0.578 9.592 15130 Z= 0.286 Chirality : 0.040 0.173 1627 Planarity : 0.004 0.038 1821 Dihedral : 15.279 125.186 1960 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.60 % Allowed : 12.58 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.24), residues: 1215 helix: 1.01 (0.31), residues: 324 sheet: -0.05 (0.41), residues: 162 loop : -1.61 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1509 HIS 0.005 0.001 HIS A1279 PHE 0.028 0.002 PHE A1277 TYR 0.011 0.001 TYR A 958 ARG 0.009 0.000 ARG A1243 Details of bonding type rmsd hydrogen bonds : bond 0.03770 ( 293) hydrogen bonds : angle 4.93455 ( 828) metal coordination : bond 0.00495 ( 15) metal coordination : angle 2.94560 ( 15) covalent geometry : bond 0.00365 (11082) covalent geometry : angle 0.57034 (15115) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3132.11 seconds wall clock time: 56 minutes 3.98 seconds (3363.98 seconds total)