Starting phenix.real_space_refine on Wed Aug 5 15:59:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gna_34158/08_2026/8gna_34158.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gna_34158/08_2026/8gna_34158.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gna_34158/08_2026/8gna_34158.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gna_34158/08_2026/8gna_34158.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8gna_34158/08_2026/8gna_34158.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gna_34158/08_2026/8gna_34158.cif" model { file = "/net/cci-nas-00/data/ceres_data/8gna_34158/08_2026/8gna_34158.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gna_34158/08_2026/8gna_34158.cif" } resolution = 2.8 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= 0.000 sd= 1.000 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 49 5.49 5 S 31 5.16 5 C 6394 2.51 5 N 1799 2.21 5 O 1980 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10257 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1188, 9213 Classifications: {'peptide': 1188} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 59, 'TRANS': 1128} Chain breaks: 16 Unresolved non-hydrogen bonds: 394 Unresolved non-hydrogen angles: 485 Unresolved non-hydrogen dihedrals: 305 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 31, 'GLN:plan1': 5, 'ASN:plan1': 12, 'ASP:plan': 23, 'ARG:plan': 6, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 285 Chain: "C" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 666 Classifications: {'RNAv2': 32} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 9, 'rna3p_pur': 1, 'rna3p_pyr': 12} Link IDs: {'rna2p': 18, 'rna3p': 13} Chain: "J" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 374 Classifications: {'RNAv2': 17} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 12, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 14} 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 3206 SG CYS A 491 47.308 52.523 101.159 1.00 43.52 S ATOM 3274 SG CYS A 501 47.555 52.621 104.833 1.00 47.64 S ATOM 3288 SG CYS A 503 44.681 54.365 103.302 1.00 45.64 S ATOM 3310 SG CYS A 506 44.605 50.647 103.129 1.00 40.94 S ATOM 644 SG CYS A 88 39.765 40.427 132.198 1.00 65.88 S ATOM 852 SG CYS A 121 40.171 38.526 135.417 1.00 79.39 S ATOM 883 SG CYS A 127 36.773 38.593 133.814 1.00 67.21 S ATOM 907 SG CYS A 130 39.760 36.779 132.037 1.00 64.85 S ATOM 5172 SG CYS A 750 56.150 57.879 73.817 1.00 56.51 S ATOM 5185 SG CYS A 752 53.020 59.011 72.136 1.00 48.44 S ATOM 5207 SG CYS A 755 52.874 55.748 73.926 1.00 45.65 S ATOM 7073 SG CYS A1018 51.365 43.491 39.396 1.00 41.19 S ATOM 7231 SG CYS A1406 53.584 44.149 42.474 1.00 48.81 S ATOM 7282 SG CYS A1414 53.454 46.347 39.428 1.00 40.01 S ATOM 7299 SG CYS A1417 50.257 45.905 41.964 1.00 35.80 S Time building chain proxies: 1.98, per 1000 atoms: 0.19 Number of scatterers: 10257 At special positions: 0 Unit cell: (71.25, 84.55, 148.2, 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 31 16.00 P 49 15.00 O 1980 8.00 N 1799 7.00 C 6394 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: 0.83 Conformation dependent library (CDL) restraints added in 325.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 503 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 501 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 491 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 506 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 88 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 121 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 130 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 127 " pdb=" ZN A1803 " pdb="ZN ZN A1803 " - pdb=" ND1 HIS A 747 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 752 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 755 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 750 " pdb=" ZN A1804 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1018 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1406 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1414 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1417 " Number of angles added : 21 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2174 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 22 sheets defined 30.9% alpha, 22.1% beta 12 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 32 through 38 removed outlier: 3.569A pdb=" N MET A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 78 Processing helix chain 'A' and resid 127 through 134 Processing helix chain 'A' and resid 168 through 173 removed outlier: 3.544A pdb=" N ILE A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 216 through 227 Processing helix chain 'A' and resid 270 through 288 Processing helix chain 'A' and resid 292 through 303 Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 338 through 350 Processing helix chain 'A' and resid 354 through 373 Processing helix chain 'A' and resid 471 through 488 Processing helix chain 'A' and resid 503 through 511 removed outlier: 3.540A pdb=" N GLU A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG A 511 " --> pdb=" O ILE A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 580 Processing helix chain 'A' and resid 594 through 598 Processing helix chain 'A' and resid 618 through 624 removed outlier: 3.641A pdb=" N ILE A 622 " --> pdb=" O ILE A 618 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS A 623 " --> pdb=" O ASN A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 628 Processing helix chain 'A' and resid 630 through 637 removed outlier: 3.713A pdb=" N LEU A 634 " --> pdb=" O LYS A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 657 removed outlier: 3.652A pdb=" N CYS A 657 " --> pdb=" O GLU A 654 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 654 through 657' Processing helix chain 'A' and resid 658 through 665 Processing helix chain 'A' and resid 686 through 693 removed outlier: 3.570A pdb=" N LEU A 691 " --> pdb=" O THR A 687 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR A 692 " --> pdb=" O ILE A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 740 removed outlier: 3.606A pdb=" N PHE A 731 " --> pdb=" O HIS A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 759 Processing helix chain 'A' and resid 831 through 848 removed outlier: 3.551A pdb=" N ALA A 841 " --> pdb=" O LEU A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 878 Processing helix chain 'A' and resid 910 through 914 removed outlier: 4.141A pdb=" N ASP A 914 " --> pdb=" O PRO A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1016 Processing helix chain 'A' and resid 1395 through 1399 removed outlier: 3.750A pdb=" N LEU A1399 " --> pdb=" O GLY A1396 " (cutoff:3.500A) Processing helix chain 'A' and resid 1408 through 1412 Processing helix chain 'A' and resid 1414 through 1420 Processing helix chain 'A' and resid 1463 through 1468 removed outlier: 4.100A pdb=" N SER A1467 " --> pdb=" O ARG A1463 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1493 removed outlier: 3.713A pdb=" N ILE A1490 " --> pdb=" O GLY A1486 " (cutoff:3.500A) Processing helix chain 'A' and resid 1528 through 1540 removed outlier: 3.794A pdb=" N GLY A1533 " --> pdb=" O GLU A1529 " (cutoff:3.500A) Processing helix chain 'A' and resid 1583 through 1588 Processing helix chain 'A' and resid 1590 through 1601 Processing helix chain 'A' and resid 1615 through 1618 Processing helix chain 'A' and resid 1619 through 1630 Processing helix chain 'A' and resid 1675 through 1681 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 22 removed outlier: 6.754A pdb=" N SER A 56 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 22 removed outlier: 6.754A pdb=" N SER A 56 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A 238 " --> pdb=" O GLU A 11 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 111 removed outlier: 5.914A pdb=" N THR A 110 " --> pdb=" O VAL A 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 176 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 180 through 181 removed outlier: 7.131A pdb=" N ARG A 180 " --> pdb=" O LYS A 189 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 512 through 514 Processing sheet with id=AA8, first strand: chain 'A' and resid 512 through 514 removed outlier: 4.548A pdb=" N ARG A 421 " --> pdb=" O ASP A 606 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ASP A 606 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LYS A 423 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU A 604 " --> pdb=" O LYS A 423 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 431 through 432 removed outlier: 4.463A pdb=" N ASN A 459 " --> pdb=" O VAL A 432 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 469 through 470 Processing sheet with id=AB2, first strand: chain 'A' and resid 526 through 533 removed outlier: 6.429A pdb=" N SER A 544 " --> pdb=" O ALA A 532 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 721 through 722 removed outlier: 4.135A pdb=" N GLU A 773 " --> pdb=" O LYS A 821 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 721 through 722 removed outlier: 4.135A pdb=" N GLU A 773 " --> pdb=" O LYS A 821 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N GLN A 673 " --> pdb=" O ILE A 868 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ILE A 868 " --> pdb=" O GLN A 673 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N THR A 675 " --> pdb=" O ILE A 866 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ILE A 866 " --> pdb=" O THR A 675 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLU A 677 " --> pdb=" O ALA A 864 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 699 through 700 removed outlier: 6.956A pdb=" N ALA A 699 " --> pdb=" O TYR A 808 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ALA A 803 " --> pdb=" O ALA A 791 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 920 through 921 Processing sheet with id=AB7, first strand: chain 'A' and resid 924 through 927 Processing sheet with id=AB8, first strand: chain 'A' and resid 1429 through 1431 removed outlier: 3.733A pdb=" N ASN A1516 " --> pdb=" O THR A 960 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N SER A 951 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR A1569 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LYS A 953 " --> pdb=" O LEU A1567 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU A1567 " --> pdb=" O LYS A 953 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1429 through 1431 removed outlier: 3.733A pdb=" N ASN A1516 " --> pdb=" O THR A 960 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N SER A 951 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR A1569 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LYS A 953 " --> pdb=" O LEU A1567 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU A1567 " --> pdb=" O LYS A 953 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 967 through 968 removed outlier: 4.327A pdb=" N LYS A 988 " --> pdb=" O ASP A 968 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 991 through 992 removed outlier: 3.555A pdb=" N GLU A 995 " --> pdb=" O ILE A 992 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1453 through 1455 Processing sheet with id=AC4, first strand: chain 'A' and resid 1647 through 1648 removed outlier: 6.492A pdb=" N VAL A1647 " --> pdb=" O TYR A1663 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 353 hydrogen bonds defined for protein. 969 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 31 hydrogen bonds 58 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 2.49 Time building geometry restraints manager: 1.06 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: 2967 1.34 - 1.45: 2028 1.45 - 1.57: 5460 1.57 - 1.69: 96 1.69 - 1.81: 42 Bond restraints: 10593 Sorted by residual: bond pdb=" P A C -17 " pdb=" OP1 A C -17 " ideal model delta sigma weight residual 1.485 1.516 -0.031 2.00e-02 2.50e+03 2.40e+00 bond pdb=" P A C -17 " pdb=" OP2 A C -17 " ideal model delta sigma weight residual 1.485 1.515 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" P C C -16 " pdb=" OP1 C C -16 " ideal model delta sigma weight residual 1.485 1.510 -0.025 2.00e-02 2.50e+03 1.58e+00 bond pdb=" C1' A C -17 " pdb=" N9 A C -17 " ideal model delta sigma weight residual 1.478 1.455 0.023 2.00e-02 2.50e+03 1.32e+00 bond pdb=" P C C -16 " pdb=" OP2 C C -16 " ideal model delta sigma weight residual 1.485 1.508 -0.023 2.00e-02 2.50e+03 1.30e+00 ... (remaining 10588 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.20: 14409 3.20 - 6.40: 140 6.40 - 9.60: 4 9.60 - 12.80: 1 12.80 - 16.00: 1 Bond angle restraints: 14555 Sorted by residual: angle pdb=" C3' C C -16 " pdb=" O3' C C -16 " pdb=" P U C -15 " ideal model delta sigma weight residual 119.70 103.70 16.00 1.20e+00 6.94e-01 1.78e+02 angle pdb=" C3' A C -17 " pdb=" O3' A C -17 " pdb=" P C C -16 " ideal model delta sigma weight residual 119.70 110.10 9.60 1.20e+00 6.94e-01 6.40e+01 angle pdb=" C3' U C -14 " pdb=" O3' U C -14 " pdb=" P A C -13 " ideal model delta sigma weight residual 119.70 112.54 7.16 1.20e+00 6.94e-01 3.56e+01 angle pdb=" C THR A1423 " pdb=" N ASP A1424 " pdb=" CA ASP A1424 " ideal model delta sigma weight residual 121.54 128.27 -6.73 1.91e+00 2.74e-01 1.24e+01 angle pdb=" O3' C C -16 " pdb=" P U C -15 " pdb=" O5' U C -15 " ideal model delta sigma weight residual 104.00 98.62 5.38 1.90e+00 2.77e-01 8.01e+00 ... (remaining 14550 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 5345 17.33 - 34.67: 560 34.67 - 52.00: 144 52.00 - 69.34: 85 69.34 - 86.67: 28 Dihedral angle restraints: 6162 sinusoidal: 2778 harmonic: 3384 Sorted by residual: dihedral pdb=" C4' G C 11 " pdb=" C3' G C 11 " pdb=" C2' G C 11 " pdb=" C1' G C 11 " ideal model delta sinusoidal sigma weight residual 36.34 -37.80 74.15 1 3.10e+00 1.04e-01 7.26e+02 dihedral pdb=" C4' U J 36 " pdb=" C3' U J 36 " pdb=" C2' U J 36 " pdb=" C1' U J 36 " ideal model delta sinusoidal sigma weight residual 36.34 -36.78 73.12 1 3.10e+00 1.04e-01 7.09e+02 dihedral pdb=" C4' A C -2 " pdb=" C3' A C -2 " pdb=" C2' A C -2 " pdb=" C1' A C -2 " ideal model delta sinusoidal sigma weight residual 36.34 -36.31 72.65 1 3.10e+00 1.04e-01 7.01e+02 ... (remaining 6159 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.163: 1533 0.163 - 0.326: 91 0.326 - 0.490: 2 0.490 - 0.653: 2 0.653 - 0.816: 1 Chirality restraints: 1629 Sorted by residual: chirality pdb=" P A C -17 " pdb=" OP1 A C -17 " pdb=" OP2 A C -17 " pdb=" O5' A C -17 " both_signs ideal model delta sigma weight residual True 2.17 -2.99 -0.82 2.00e-01 2.50e+01 1.66e+01 chirality pdb=" P U C -14 " pdb=" OP1 U C -14 " pdb=" OP2 U C -14 " pdb=" O5' U C -14 " both_signs ideal model delta sigma weight residual True 2.17 -2.74 -0.57 2.00e-01 2.50e+01 8.00e+00 chirality pdb=" P C C -16 " pdb=" OP1 C C -16 " pdb=" OP2 C C -16 " pdb=" O5' C C -16 " both_signs ideal model delta sigma weight residual True 2.17 -2.71 -0.53 2.00e-01 2.50e+01 7.13e+00 ... (remaining 1626 not shown) Planarity restraints: 1676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U C -15 " 0.034 2.00e-02 2.50e+03 1.88e-02 7.94e+00 pdb=" N1 U C -15 " -0.033 2.00e-02 2.50e+03 pdb=" C2 U C -15 " -0.001 2.00e-02 2.50e+03 pdb=" O2 U C -15 " -0.015 2.00e-02 2.50e+03 pdb=" N3 U C -15 " 0.019 2.00e-02 2.50e+03 pdb=" C4 U C -15 " 0.011 2.00e-02 2.50e+03 pdb=" O4 U C -15 " -0.003 2.00e-02 2.50e+03 pdb=" C5 U C -15 " 0.002 2.00e-02 2.50e+03 pdb=" C6 U C -15 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G C 11 " -0.030 2.00e-02 2.50e+03 1.45e-02 6.34e+00 pdb=" N9 G C 11 " 0.039 2.00e-02 2.50e+03 pdb=" C8 G C 11 " 0.000 2.00e-02 2.50e+03 pdb=" N7 G C 11 " -0.003 2.00e-02 2.50e+03 pdb=" C5 G C 11 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G C 11 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G C 11 " -0.008 2.00e-02 2.50e+03 pdb=" N1 G C 11 " -0.000 2.00e-02 2.50e+03 pdb=" C2 G C 11 " -0.000 2.00e-02 2.50e+03 pdb=" N2 G C 11 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G C 11 " 0.002 2.00e-02 2.50e+03 pdb=" C4 G C 11 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A C -2 " -0.030 2.00e-02 2.50e+03 1.37e-02 5.19e+00 pdb=" N9 A C -2 " 0.032 2.00e-02 2.50e+03 pdb=" C8 A C -2 " -0.000 2.00e-02 2.50e+03 pdb=" N7 A C -2 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A C -2 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A C -2 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A C -2 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A C -2 " -0.004 2.00e-02 2.50e+03 pdb=" C2 A C -2 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A C -2 " 0.006 2.00e-02 2.50e+03 pdb=" C4 A C -2 " 0.006 2.00e-02 2.50e+03 ... (remaining 1673 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 328 2.68 - 3.23: 9850 3.23 - 3.79: 17440 3.79 - 4.34: 24763 4.34 - 4.90: 39241 Nonbonded interactions: 91622 Sorted by model distance: nonbonded pdb=" OH TYR A 922 " pdb=" OP2 C C 15 " model vdw 2.125 3.040 nonbonded pdb=" O GLY A 186 " pdb=" O2' C C -1 " model vdw 2.173 3.040 nonbonded pdb=" O ASP A 801 " pdb=" O2' C J 28 " model vdw 2.195 3.040 nonbonded pdb=" OE1 GLU A 465 " pdb=" NH2 ARG A 467 " model vdw 2.204 3.120 nonbonded pdb=" OH TYR A 934 " pdb=" OE1 GLU A 936 " model vdw 2.205 3.040 ... (remaining 91617 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.640 Find NCS groups from input model: 0.050 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:8.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 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 10609 Z= 0.128 Angle : 0.734 15.996 14576 Z= 0.350 Chirality : 0.077 0.816 1629 Planarity : 0.004 0.050 1676 Dihedral : 17.135 86.674 3988 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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: -0.88 (0.24), residues: 1154 helix: 0.25 (0.31), residues: 289 sheet: -0.69 (0.43), residues: 141 loop : -0.91 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 212 TYR 0.012 0.001 TYR A1590 PHE 0.017 0.001 PHE A 284 TRP 0.011 0.001 TRP A 82 HIS 0.003 0.001 HIS A1621 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (10593) covalent geometry : angle 0.70810 / 0.35 (14555) hydrogen bonds : bond 0.22501 / 15.34 ( 346) hydrogen bonds : angle 9.07327 / 6.80 ( 1027) metal coordination : bond 0.01176 / 0.89 ( 16) metal coordination : angle 5.11837 / 3.40 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.354 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.4945 time to fit residues: 83.3035 Evaluate side-chains 104 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 HIS ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 ASN A 696 ASN A 786 HIS ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1516 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.166968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.145289 restraints weight = 10955.402| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.59 r_work: 0.3664 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3543 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 10609 Z= 0.248 Angle : 1.119 20.930 14576 Z= 0.470 Chirality : 0.101 1.341 1629 Planarity : 0.005 0.051 1676 Dihedral : 14.163 162.168 1857 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.38 % Allowed : 11.66 % Favored : 85.96 % 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: -0.91 (0.24), residues: 1154 helix: 0.31 (0.29), residues: 310 sheet: -0.46 (0.39), residues: 172 loop : -1.08 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 472 TYR 0.021 0.002 TYR A1595 PHE 0.018 0.002 PHE A 284 TRP 0.018 0.002 TRP A 82 HIS 0.006 0.001 HIS A 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.25 (10593) covalent geometry : angle 1.09114 / 0.47 (14555) hydrogen bonds : bond 0.05393 / 3.51 ( 346) hydrogen bonds : angle 6.18206 / 4.56 ( 1027) metal coordination : bond 0.01085 / 0.76 ( 16) metal coordination : angle 6.65357 / 4.34 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.293 Fit side-chains REVERT: A 351 LYS cc_start: 0.7825 (mmmm) cc_final: 0.7501 (mmtt) REVERT: A 498 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7417 (mp-120) REVERT: A 611 GLU cc_start: 0.8727 (pt0) cc_final: 0.8403 (pt0) REVERT: A 717 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7668 (mt-10) REVERT: A 1595 TYR cc_start: 0.8323 (t80) cc_final: 0.8115 (t80) outliers start: 22 outliers final: 6 residues processed: 132 average time/residue: 0.5255 time to fit residues: 75.1006 Evaluate side-chains 104 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 1509 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 17 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 65 optimal weight: 0.0070 chunk 90 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 ASN A 109 HIS A 696 ASN ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.169244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.147833 restraints weight = 11023.634| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 1.59 r_work: 0.3682 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3562 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10609 Z= 0.177 Angle : 0.888 15.081 14576 Z= 0.384 Chirality : 0.075 0.756 1629 Planarity : 0.004 0.048 1676 Dihedral : 14.596 159.023 1857 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.59 % Allowed : 14.25 % Favored : 83.15 % 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: -0.91 (0.24), residues: 1154 helix: 0.43 (0.30), residues: 314 sheet: -0.55 (0.38), residues: 174 loop : -1.14 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 476 TYR 0.012 0.001 TYR A1595 PHE 0.013 0.001 PHE A1520 TRP 0.010 0.001 TRP A 82 HIS 0.005 0.001 HIS A 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (10593) covalent geometry : angle 0.86195 / 0.38 (14555) hydrogen bonds : bond 0.05175 / 3.38 ( 346) hydrogen bonds : angle 5.62989 / 4.14 ( 1027) metal coordination : bond 0.01326 / 0.88 ( 16) metal coordination : angle 5.63742 / 3.67 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.370 Fit side-chains REVERT: A 36 MET cc_start: 0.8696 (mmm) cc_final: 0.8466 (mmt) REVERT: A 717 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7632 (mt-10) REVERT: A 830 PHE cc_start: 0.7189 (m-10) cc_final: 0.6900 (m-10) REVERT: A 1435 LYS cc_start: 0.8279 (ptpp) cc_final: 0.7694 (ptpt) outliers start: 24 outliers final: 10 residues processed: 129 average time/residue: 0.5110 time to fit residues: 71.6823 Evaluate side-chains 106 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 778 ASN Chi-restraints excluded: chain A residue 880 ILE Chi-restraints excluded: chain A residue 1509 THR Chi-restraints excluded: chain A residue 1639 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 25 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 88 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 HIS A 350 ASN A 502 ASN A 696 ASN ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.168196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.146672 restraints weight = 11094.723| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 1.60 r_work: 0.3668 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10609 Z= 0.185 Angle : 0.861 15.770 14576 Z= 0.375 Chirality : 0.071 0.721 1629 Planarity : 0.004 0.048 1676 Dihedral : 14.810 159.140 1857 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.13 % Allowed : 15.77 % Favored : 81.10 % 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: 1154 helix: 0.36 (0.29), residues: 319 sheet: -0.63 (0.37), residues: 176 loop : -1.18 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 476 TYR 0.012 0.001 TYR A1595 PHE 0.014 0.001 PHE A1520 TRP 0.010 0.001 TRP A 612 HIS 0.006 0.001 HIS A 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (10593) covalent geometry : angle 0.83395 / 0.37 (14555) hydrogen bonds : bond 0.04528 / 2.97 ( 346) hydrogen bonds : angle 5.38277 / 3.95 ( 1027) metal coordination : bond 0.00920 / 0.66 ( 16) metal coordination : angle 5.70117 / 3.71 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 0.277 Fit side-chains REVERT: A 36 MET cc_start: 0.8644 (mmm) cc_final: 0.8391 (mmt) REVERT: A 717 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7614 (mt-10) REVERT: A 783 LEU cc_start: 0.8656 (tp) cc_final: 0.8456 (tp) REVERT: A 830 PHE cc_start: 0.7005 (m-10) cc_final: 0.6765 (m-10) REVERT: A 950 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8051 (tt) outliers start: 29 outliers final: 13 residues processed: 135 average time/residue: 0.5172 time to fit residues: 75.6018 Evaluate side-chains 111 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 880 ILE Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 1507 VAL Chi-restraints excluded: chain A residue 1509 THR Chi-restraints excluded: chain A residue 1639 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 35 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 97 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 HIS A 502 ASN ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.160895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.139012 restraints weight = 11189.205| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.60 r_work: 0.3581 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 10609 Z= 0.303 Angle : 0.985 18.578 14576 Z= 0.426 Chirality : 0.078 0.848 1629 Planarity : 0.005 0.053 1676 Dihedral : 14.884 156.353 1857 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 4.43 % Allowed : 16.31 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.22 (0.24), residues: 1154 helix: 0.12 (0.29), residues: 320 sheet: -0.96 (0.35), residues: 195 loop : -1.24 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 467 TYR 0.018 0.002 TYR A1595 PHE 0.020 0.002 PHE A1520 TRP 0.015 0.002 TRP A 612 HIS 0.008 0.002 HIS A 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00704 / 0.30 (10593) covalent geometry : angle 0.94794 / 0.42 (14555) hydrogen bonds : bond 0.04855 / 3.15 ( 346) hydrogen bonds : angle 5.58857 / 4.10 ( 1027) metal coordination : bond 0.01077 / 0.73 ( 16) metal coordination : angle 7.06850 / 4.61 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 92 time to evaluate : 0.335 Fit side-chains REVERT: A 36 MET cc_start: 0.8670 (mmm) cc_final: 0.8470 (mmt) REVERT: A 498 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7297 (mp-120) REVERT: A 567 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8001 (tttp) REVERT: A 830 PHE cc_start: 0.7293 (m-10) cc_final: 0.7093 (m-10) REVERT: A 950 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8054 (tt) outliers start: 41 outliers final: 17 residues processed: 125 average time/residue: 0.4433 time to fit residues: 60.8909 Evaluate side-chains 102 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 567 LYS Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 778 ASN Chi-restraints excluded: chain A residue 880 ILE Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 1435 LYS Chi-restraints excluded: chain A residue 1507 VAL Chi-restraints excluded: chain A residue 1509 THR Chi-restraints excluded: chain A residue 1639 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 19 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 98 optimal weight: 0.0980 chunk 61 optimal weight: 0.5980 chunk 120 optimal weight: 1.9990 chunk 96 optimal weight: 0.4980 chunk 45 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 HIS A 502 ASN ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.168673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.147527 restraints weight = 11146.209| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 1.57 r_work: 0.3674 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10609 Z= 0.163 Angle : 0.832 13.766 14576 Z= 0.364 Chirality : 0.068 0.672 1629 Planarity : 0.004 0.053 1676 Dihedral : 14.898 159.475 1857 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.24 % Allowed : 18.14 % Favored : 78.62 % 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: -1.04 (0.24), residues: 1154 helix: 0.41 (0.29), residues: 318 sheet: -0.96 (0.35), residues: 195 loop : -1.15 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 476 TYR 0.017 0.001 TYR A1595 PHE 0.016 0.001 PHE A 945 TRP 0.013 0.001 TRP A 612 HIS 0.004 0.001 HIS A 727 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (10593) covalent geometry : angle 0.80705 / 0.36 (14555) hydrogen bonds : bond 0.04378 / 2.88 ( 346) hydrogen bonds : angle 5.28579 / 3.86 ( 1027) metal coordination : bond 0.01055 / 0.82 ( 16) metal coordination : angle 5.36059 / 3.48 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.355 Fit side-chains REVERT: A 194 THR cc_start: 0.8206 (OUTLIER) cc_final: 0.7945 (p) REVERT: A 783 LEU cc_start: 0.8661 (tp) cc_final: 0.8425 (tp) REVERT: A 830 PHE cc_start: 0.6900 (OUTLIER) cc_final: 0.6611 (m-10) REVERT: A 950 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7943 (tt) outliers start: 30 outliers final: 15 residues processed: 135 average time/residue: 0.4362 time to fit residues: 64.5148 Evaluate side-chains 110 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 778 ASN Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 880 ILE Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 1507 VAL Chi-restraints excluded: chain A residue 1509 THR Chi-restraints excluded: chain A residue 1511 VAL Chi-restraints excluded: chain A residue 1639 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 96 optimal weight: 0.4980 chunk 83 optimal weight: 2.9990 chunk 65 optimal weight: 0.0070 chunk 95 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 HIS A 502 ASN A 696 ASN ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.169226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.147952 restraints weight = 10923.861| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 1.56 r_work: 0.3677 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3559 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10609 Z= 0.167 Angle : 0.831 14.259 14576 Z= 0.364 Chirality : 0.068 0.665 1629 Planarity : 0.004 0.053 1676 Dihedral : 14.843 159.254 1857 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.67 % Allowed : 18.57 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.24), residues: 1154 helix: 0.43 (0.29), residues: 321 sheet: -0.80 (0.37), residues: 177 loop : -1.21 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 476 TYR 0.018 0.001 TYR A1595 PHE 0.015 0.001 PHE A1520 TRP 0.012 0.001 TRP A 612 HIS 0.004 0.001 HIS A 789 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (10593) covalent geometry : angle 0.80764 / 0.36 (14555) hydrogen bonds : bond 0.04201 / 2.73 ( 346) hydrogen bonds : angle 5.17147 / 3.77 ( 1027) metal coordination : bond 0.00929 / 0.70 ( 16) metal coordination : angle 5.23606 / 3.38 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 0.404 Fit side-chains REVERT: A 31 LYS cc_start: 0.8530 (mppt) cc_final: 0.8314 (mptt) REVERT: A 36 MET cc_start: 0.8684 (mmm) cc_final: 0.8458 (mmt) REVERT: A 194 THR cc_start: 0.8198 (OUTLIER) cc_final: 0.7983 (p) REVERT: A 783 LEU cc_start: 0.8659 (tp) cc_final: 0.8443 (tp) REVERT: A 830 PHE cc_start: 0.6800 (OUTLIER) cc_final: 0.6496 (m-10) REVERT: A 950 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.8012 (tt) REVERT: A 1435 LYS cc_start: 0.8198 (ptpp) cc_final: 0.7619 (ptpt) outliers start: 34 outliers final: 15 residues processed: 129 average time/residue: 0.4200 time to fit residues: 59.2089 Evaluate side-chains 112 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 778 ASN Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 880 ILE Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 1507 VAL Chi-restraints excluded: chain A residue 1509 THR Chi-restraints excluded: chain A residue 1511 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 0.0870 chunk 7 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN A 109 HIS A 179 ASN A 696 ASN ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.168825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.147461 restraints weight = 11056.108| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 1.57 r_work: 0.3670 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10609 Z= 0.176 Angle : 0.836 14.384 14576 Z= 0.367 Chirality : 0.068 0.661 1629 Planarity : 0.004 0.053 1676 Dihedral : 14.853 159.439 1857 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.81 % Allowed : 19.55 % Favored : 77.65 % 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: 1154 helix: 0.42 (0.29), residues: 322 sheet: -0.85 (0.36), residues: 177 loop : -1.23 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 476 TYR 0.015 0.001 TYR A1595 PHE 0.015 0.001 PHE A1520 TRP 0.013 0.001 TRP A 612 HIS 0.004 0.001 HIS A 789 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (10593) covalent geometry : angle 0.81188 / 0.36 (14555) hydrogen bonds : bond 0.04185 / 2.71 ( 346) hydrogen bonds : angle 5.13897 / 3.75 ( 1027) metal coordination : bond 0.00854 / 0.63 ( 16) metal coordination : angle 5.33185 / 3.44 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.362 Fit side-chains REVERT: A 36 MET cc_start: 0.8641 (mmm) cc_final: 0.8398 (mmt) REVERT: A 194 THR cc_start: 0.8232 (OUTLIER) cc_final: 0.8017 (p) REVERT: A 783 LEU cc_start: 0.8654 (tp) cc_final: 0.8445 (tp) REVERT: A 830 PHE cc_start: 0.6794 (OUTLIER) cc_final: 0.6490 (m-10) REVERT: A 950 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.8016 (tt) REVERT: A 1435 LYS cc_start: 0.8152 (ptpp) cc_final: 0.7582 (ptpt) outliers start: 26 outliers final: 15 residues processed: 128 average time/residue: 0.4663 time to fit residues: 65.1797 Evaluate side-chains 118 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 778 ASN Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 880 ILE Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 1507 VAL Chi-restraints excluded: chain A residue 1509 THR Chi-restraints excluded: chain A residue 1511 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 59 optimal weight: 2.9990 chunk 108 optimal weight: 0.0000 chunk 33 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 47 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 57.4762 > 50:) chunk 53 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN A 109 HIS A 179 ASN A 696 ASN ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.166840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.145196 restraints weight = 11039.062| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 1.60 r_work: 0.3653 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10609 Z= 0.204 Angle : 0.866 15.500 14576 Z= 0.379 Chirality : 0.070 0.670 1629 Planarity : 0.005 0.053 1676 Dihedral : 14.879 159.087 1857 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 2.70 % Allowed : 19.98 % Favored : 77.32 % 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: -1.08 (0.24), residues: 1154 helix: 0.40 (0.29), residues: 319 sheet: -0.95 (0.35), residues: 195 loop : -1.21 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 467 TYR 0.027 0.002 TYR A1595 PHE 0.017 0.002 PHE A1520 TRP 0.013 0.001 TRP A 612 HIS 0.005 0.001 HIS A 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.20 (10593) covalent geometry : angle 0.84004 / 0.38 (14555) hydrogen bonds : bond 0.04246 / 2.74 ( 346) hydrogen bonds : angle 5.16499 / 3.76 ( 1027) metal coordination : bond 0.00832 / 0.59 ( 16) metal coordination : angle 5.57468 / 3.61 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.351 Fit side-chains REVERT: A 36 MET cc_start: 0.8680 (mmm) cc_final: 0.8438 (mmt) REVERT: A 194 THR cc_start: 0.8234 (OUTLIER) cc_final: 0.8023 (p) REVERT: A 830 PHE cc_start: 0.6881 (OUTLIER) cc_final: 0.6585 (m-10) REVERT: A 950 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8037 (tt) REVERT: A 1435 LYS cc_start: 0.8194 (ptpp) cc_final: 0.7289 (mttt) outliers start: 25 outliers final: 15 residues processed: 122 average time/residue: 0.4632 time to fit residues: 61.8623 Evaluate side-chains 114 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 778 ASN Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 880 ILE Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 1507 VAL Chi-restraints excluded: chain A residue 1509 THR Chi-restraints excluded: chain A residue 1511 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 77 optimal weight: 0.2980 chunk 87 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 17 optimal weight: 0.0980 chunk 106 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN A 109 HIS A 179 ASN ** A 455 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 ASN ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.171067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.149898 restraints weight = 10896.677| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 1.56 r_work: 0.3696 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10609 Z= 0.158 Angle : 0.813 13.354 14576 Z= 0.359 Chirality : 0.066 0.659 1629 Planarity : 0.004 0.051 1676 Dihedral : 14.900 160.227 1857 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.38 % Allowed : 20.63 % Favored : 77.00 % 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: -1.04 (0.24), residues: 1154 helix: 0.48 (0.29), residues: 322 sheet: -0.81 (0.36), residues: 177 loop : -1.27 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 476 TYR 0.013 0.001 TYR A 925 PHE 0.014 0.001 PHE A1520 TRP 0.012 0.001 TRP A 612 HIS 0.004 0.001 HIS A 727 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (10593) covalent geometry : angle 0.79145 / 0.36 (14555) hydrogen bonds : bond 0.04114 / 2.67 ( 346) hydrogen bonds : angle 5.05722 / 3.69 ( 1027) metal coordination : bond 0.00940 / 0.72 ( 16) metal coordination : angle 4.93643 / 3.18 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.365 Fit side-chains REVERT: A 36 MET cc_start: 0.8658 (mmm) cc_final: 0.8415 (mmt) REVERT: A 357 LYS cc_start: 0.7727 (mptp) cc_final: 0.7369 (ttmm) REVERT: A 830 PHE cc_start: 0.6733 (OUTLIER) cc_final: 0.6473 (m-10) REVERT: A 950 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7998 (tt) REVERT: A 1435 LYS cc_start: 0.8094 (ptpp) cc_final: 0.7209 (mttt) outliers start: 22 outliers final: 14 residues processed: 119 average time/residue: 0.4576 time to fit residues: 59.5129 Evaluate side-chains 112 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 778 ASN Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 880 ILE Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 1507 VAL Chi-restraints excluded: chain A residue 1509 THR Chi-restraints excluded: chain A residue 1511 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 54 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 94 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN A 109 HIS A 179 ASN A 696 ASN ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.169037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.147681 restraints weight = 11099.203| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 1.58 r_work: 0.3671 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10609 Z= 0.181 Angle : 0.835 14.270 14576 Z= 0.367 Chirality : 0.068 0.663 1629 Planarity : 0.005 0.052 1676 Dihedral : 14.898 159.858 1857 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 2.16 % Allowed : 21.60 % Favored : 76.24 % 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: -1.06 (0.24), residues: 1154 helix: 0.47 (0.29), residues: 322 sheet: -0.80 (0.36), residues: 177 loop : -1.29 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 467 TYR 0.015 0.002 TYR A1595 PHE 0.015 0.001 PHE A1520 TRP 0.012 0.001 TRP A 612 HIS 0.004 0.001 HIS A 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (10593) covalent geometry : angle 0.81227 / 0.37 (14555) hydrogen bonds : bond 0.04122 / 2.66 ( 346) hydrogen bonds : angle 5.05709 / 3.69 ( 1027) metal coordination : bond 0.00831 / 0.61 ( 16) metal coordination : angle 5.20509 / 3.35 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3114.51 seconds wall clock time: 54 minutes 4.15 seconds (3244.15 seconds total)