Starting phenix.real_space_refine on Thu Jul 2 22:17:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gna_34158/07_2026/8gna_34158.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gna_34158/07_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_34158/07_2026/8gna_34158.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gna_34158/07_2026/8gna_34158.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8gna_34158/07_2026/8gna_34158.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gna_34158/07_2026/8gna_34158.cif" model { file = "/net/cci-nas-00/data/ceres_data/8gna_34158/07_2026/8gna_34158.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gna_34158/07_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-dev-6108/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: {'RNA': 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: {'RNA': 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: 2.80, per 1000 atoms: 0.27 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: 0.92 Conformation dependent library (CDL) restraints added in 376.7 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: 1.30 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: 2.50 Time building geometry restraints manager: 1.32 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=" O5' C C -16 " pdb=" C5' C C -16 " ideal model delta sigma weight residual 1.420 1.447 -0.027 1.50e-02 4.44e+03 3.13e+00 bond pdb=" O5' A C -17 " pdb=" C5' A C -17 " ideal model delta sigma weight residual 1.420 1.445 -0.025 1.50e-02 4.44e+03 2.87e+00 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=" O5' U C -14 " pdb=" C5' U C -14 " ideal model delta sigma weight residual 1.420 1.441 -0.021 1.50e-02 4.44e+03 1.98e+00 ... (remaining 10588 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.30: 14503 3.30 - 6.60: 46 6.60 - 9.90: 4 9.90 - 13.20: 1 13.20 - 16.50: 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 120.20 103.70 16.50 1.50e+00 4.44e-01 1.21e+02 angle pdb=" C4' U C -15 " pdb=" C3' U C -15 " pdb=" C2' U C -15 " ideal model delta sigma weight residual 102.60 94.07 8.53 1.00e+00 1.00e+00 7.28e+01 angle pdb=" C3' A C -17 " pdb=" O3' A C -17 " pdb=" P C C -16 " ideal model delta sigma weight residual 120.20 110.10 10.10 1.50e+00 4.44e-01 4.54e+01 angle pdb=" C3' U C -14 " pdb=" O3' U C -14 " pdb=" P A C -13 " ideal model delta sigma weight residual 120.20 112.54 7.66 1.50e+00 4.44e-01 2.61e+01 angle pdb=" O4' U C -15 " pdb=" C4' U C -15 " pdb=" C3' U C -15 " ideal model delta sigma weight residual 104.00 99.85 4.15 1.00e+00 1.00e+00 1.72e+01 ... (remaining 14550 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.29: 6010 35.29 - 70.58: 140 70.58 - 105.87: 8 105.87 - 141.17: 2 141.17 - 176.46: 2 Dihedral angle restraints: 6162 sinusoidal: 2778 harmonic: 3384 Sorted by residual: dihedral pdb=" O4' U C -9 " pdb=" C1' U C -9 " pdb=" N1 U C -9 " pdb=" C2 U C -9 " ideal model delta sinusoidal sigma weight residual -128.00 48.46 -176.46 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U C 10 " pdb=" C1' U C 10 " pdb=" N1 U C 10 " pdb=" C2 U C 10 " ideal model delta sinusoidal sigma weight residual -128.00 39.56 -167.56 1 1.70e+01 3.46e-03 6.57e+01 dihedral pdb=" CA GLU A1589 " pdb=" C GLU A1589 " pdb=" N TYR A1590 " pdb=" CA TYR A1590 " ideal model delta harmonic sigma weight residual 180.00 158.72 21.28 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 6159 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 1601 0.116 - 0.232: 23 0.232 - 0.347: 4 0.347 - 0.463: 0 0.463 - 0.579: 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 2.41 -2.99 -0.58 2.00e-01 2.50e+01 8.38e+00 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 2.41 -2.74 -0.33 2.00e-01 2.50e+01 2.70e+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 2.41 -2.71 -0.30 2.00e-01 2.50e+01 2.21e+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: 2.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 14.410 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.400 ------------------------------------------------------------------------------- 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= 0.122 Angle : 0.607 16.496 14576 Z= 0.321 Chirality : 0.045 0.579 1629 Planarity : 0.004 0.050 1676 Dihedral : 15.035 176.458 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 0.00255 / 0.12 (10593) covalent geometry : angle 0.57587 / 0.32 (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 : 0.403 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.5760 time to fit residues: 97.0333 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 : 0.383 ------------------------------------------------------------------------------- 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: 2.9990 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 = 0.3894 r_free = 0.3894 target = 0.163061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.140326 restraints weight = 11033.710| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 1.62 r_work: 0.3600 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10609 Z= 0.221 Angle : 0.696 16.231 14576 Z= 0.341 Chirality : 0.046 0.379 1629 Planarity : 0.005 0.051 1676 Dihedral : 13.130 176.993 1857 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 2.05 % Allowed : 11.56 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.93 (0.24), residues: 1154 helix: 0.28 (0.29), residues: 312 sheet: -0.45 (0.39), residues: 172 loop : -1.10 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 467 TYR 0.021 0.002 TYR A1595 PHE 0.019 0.002 PHE A 284 TRP 0.019 0.002 TRP A 82 HIS 0.006 0.001 HIS A 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.22 (10593) covalent geometry : angle 0.64587 / 0.34 (14555) hydrogen bonds : bond 0.05021 / 3.33 ( 346) hydrogen bonds : angle 6.09987 / 4.51 ( 1027) metal coordination : bond 0.01428 / 0.92 ( 16) metal coordination : angle 6.83844 / 4.48 ( 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 134 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.398 Fit side-chains REVERT: A 498 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7439 (mp-120) REVERT: A 611 GLU cc_start: 0.8660 (pt0) cc_final: 0.8414 (pt0) REVERT: A 717 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7655 (mt-10) REVERT: A 925 TYR cc_start: 0.8002 (m-80) cc_final: 0.7785 (m-80) REVERT: A 1595 TYR cc_start: 0.8348 (t80) cc_final: 0.8127 (t80) outliers start: 19 outliers final: 6 residues processed: 128 average time/residue: 0.5355 time to fit residues: 74.2990 Evaluate side-chains 101 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 238 GLU Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 778 ASN 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: 0.6980 chunk 32 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 65 optimal weight: 0.0020 chunk 90 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 118 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.0592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 HIS ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 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 = 0.3880 r_free = 0.3880 target = 0.161882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.139107 restraints weight = 11128.238| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 1.62 r_work: 0.3585 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10609 Z= 0.209 Angle : 0.658 14.521 14576 Z= 0.325 Chirality : 0.046 0.406 1629 Planarity : 0.005 0.051 1676 Dihedral : 13.188 176.529 1857 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.67 % Allowed : 12.63 % Favored : 83.69 % 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: 0.21 (0.29), residues: 321 sheet: -0.66 (0.37), residues: 174 loop : -1.15 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 472 TYR 0.012 0.001 TYR A1595 PHE 0.016 0.002 PHE A 284 TRP 0.013 0.001 TRP A 82 HIS 0.007 0.001 HIS A 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.21 (10593) covalent geometry : angle 0.61479 / 0.32 (14555) hydrogen bonds : bond 0.04477 / 3.04 ( 346) hydrogen bonds : angle 5.67101 / 4.18 ( 1027) metal coordination : bond 0.01075 / 0.71 ( 16) metal coordination : angle 6.19216 / 4.02 ( 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 142 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 108 time to evaluate : 0.392 Fit side-chains REVERT: A 498 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7348 (mp-120) REVERT: A 567 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7859 (tttp) REVERT: A 611 GLU cc_start: 0.8622 (pt0) cc_final: 0.8335 (pt0) REVERT: A 622 ILE cc_start: 0.7626 (mp) cc_final: 0.7417 (mp) REVERT: A 717 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7630 (mt-10) REVERT: A 830 PHE cc_start: 0.7296 (m-10) cc_final: 0.7051 (m-10) REVERT: A 1435 LYS cc_start: 0.8266 (ptpp) cc_final: 0.7844 (ptmm) outliers start: 34 outliers final: 13 residues processed: 134 average time/residue: 0.5224 time to fit residues: 76.1362 Evaluate side-chains 101 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 201 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 337 THR 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 696 ASN Chi-restraints excluded: chain A residue 717 GLU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 25 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 10 optimal weight: 0.0040 chunk 88 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 HIS ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 ASN ** 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 = 0.3895 r_free = 0.3895 target = 0.163563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.140898 restraints weight = 11202.913| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 1.63 r_work: 0.3606 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10609 Z= 0.161 Angle : 0.616 12.252 14576 Z= 0.309 Chirality : 0.045 0.412 1629 Planarity : 0.004 0.049 1676 Dihedral : 13.152 175.991 1857 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % 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: -1.02 (0.24), residues: 1154 helix: 0.30 (0.29), residues: 319 sheet: -0.88 (0.35), residues: 195 loop : -1.09 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 719 TYR 0.021 0.001 TYR A1595 PHE 0.013 0.001 PHE A1520 TRP 0.011 0.001 TRP A 612 HIS 0.005 0.001 HIS A 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (10593) covalent geometry : angle 0.57982 / 0.31 (14555) hydrogen bonds : bond 0.04143 / 2.84 ( 346) hydrogen bonds : angle 5.41704 / 3.98 ( 1027) metal coordination : bond 0.00959 / 0.72 ( 16) metal coordination : angle 5.50691 / 3.55 ( 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 134 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 0.384 Fit side-chains REVERT: A 498 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7304 (mp-120) REVERT: A 717 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7663 (mt-10) REVERT: A 830 PHE cc_start: 0.7086 (m-10) cc_final: 0.6869 (m-10) REVERT: A 950 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7981 (tt) outliers start: 29 outliers final: 14 residues processed: 124 average time/residue: 0.5161 time to fit residues: 69.6270 Evaluate side-chains 111 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 237 ILE 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 498 GLN 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 717 GLU 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 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: 0.4980 chunk 77 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 HIS A 696 ASN ** 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 = 0.3859 r_free = 0.3859 target = 0.159963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.137160 restraints weight = 11182.498| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 1.62 r_work: 0.3565 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10609 Z= 0.226 Angle : 0.672 12.967 14576 Z= 0.331 Chirality : 0.047 0.428 1629 Planarity : 0.005 0.051 1676 Dihedral : 13.184 177.082 1857 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 4.00 % Allowed : 16.52 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.24), residues: 1154 helix: 0.19 (0.29), residues: 320 sheet: -0.95 (0.35), residues: 195 loop : -1.15 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 467 TYR 0.023 0.002 TYR A1595 PHE 0.018 0.002 PHE A1520 TRP 0.014 0.002 TRP A 612 HIS 0.007 0.001 HIS A 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.23 (10593) covalent geometry : angle 0.62956 / 0.33 (14555) hydrogen bonds : bond 0.04228 / 2.84 ( 346) hydrogen bonds : angle 5.43384 / 3.99 ( 1027) metal coordination : bond 0.00915 / 0.62 ( 16) metal coordination : angle 6.19183 / 4.00 ( 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 136 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 99 time to evaluate : 0.394 Fit side-chains REVERT: A 498 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7255 (mp-120) REVERT: A 717 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7759 (mt-10) REVERT: A 880 ILE cc_start: 0.6593 (OUTLIER) cc_final: 0.6116 (mt) REVERT: A 925 TYR cc_start: 0.8013 (m-80) cc_final: 0.7785 (m-80) REVERT: A 950 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7920 (tt) outliers start: 37 outliers final: 18 residues processed: 129 average time/residue: 0.5260 time to fit residues: 73.7445 Evaluate side-chains 107 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 204 THR Chi-restraints excluded: chain A residue 206 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 514 LEU 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 735 VAL 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 19 optimal weight: 0.7980 chunk 90 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 68 optimal weight: 0.2980 chunk 98 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 45 optimal weight: 0.0770 chunk 76 optimal weight: 0.5980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 ASN A 696 ASN ** 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 = 0.3933 r_free = 0.3933 target = 0.167036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.144504 restraints weight = 11230.347| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 1.63 r_work: 0.3647 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10609 Z= 0.131 Angle : 0.580 10.224 14576 Z= 0.295 Chirality : 0.044 0.427 1629 Planarity : 0.004 0.053 1676 Dihedral : 13.085 175.200 1857 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.67 % Allowed : 17.82 % Favored : 78.51 % 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: 0.46 (0.29), residues: 320 sheet: -0.90 (0.36), residues: 185 loop : -1.04 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 719 TYR 0.014 0.001 TYR A1595 PHE 0.019 0.001 PHE A 945 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 0.00293 / 0.13 (10593) covalent geometry : angle 0.55282 / 0.29 (14555) hydrogen bonds : bond 0.04079 / 2.83 ( 346) hydrogen bonds : angle 5.13002 / 3.76 ( 1027) metal coordination : bond 0.01107 / 0.87 ( 16) metal coordination : angle 4.69105 / 3.00 ( 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 152 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 118 time to evaluate : 0.398 Fit side-chains REVERT: A 194 THR cc_start: 0.8131 (OUTLIER) cc_final: 0.7918 (p) REVERT: A 357 LYS cc_start: 0.7683 (mptp) cc_final: 0.7275 (ttmm) REVERT: A 830 PHE cc_start: 0.6863 (m-10) cc_final: 0.6608 (m-10) REVERT: A 925 TYR cc_start: 0.7934 (m-80) cc_final: 0.7682 (m-80) REVERT: A 950 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7906 (tt) outliers start: 34 outliers final: 13 residues processed: 144 average time/residue: 0.4400 time to fit residues: 69.4362 Evaluate side-chains 112 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR 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 337 THR 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 778 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 17 optimal weight: 0.0980 chunk 22 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 65 optimal weight: 0.0050 chunk 95 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 434 GLN 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 = 0.3926 r_free = 0.3926 target = 0.166369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.143829 restraints weight = 11041.626| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 1.62 r_work: 0.3633 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3511 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10609 Z= 0.136 Angle : 0.590 9.699 14576 Z= 0.297 Chirality : 0.044 0.425 1629 Planarity : 0.004 0.051 1676 Dihedral : 13.018 175.907 1857 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.70 % Allowed : 19.55 % 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: -0.92 (0.24), residues: 1154 helix: 0.50 (0.29), residues: 322 sheet: -0.90 (0.35), residues: 191 loop : -1.09 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 467 TYR 0.017 0.001 TYR A1595 PHE 0.016 0.001 PHE A 945 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 0.00308 / 0.14 (10593) covalent geometry : angle 0.56426 / 0.30 (14555) hydrogen bonds : bond 0.03821 / 2.62 ( 346) hydrogen bonds : angle 5.02980 / 3.68 ( 1027) metal coordination : bond 0.00925 / 0.71 ( 16) metal coordination : angle 4.61332 / 2.94 ( 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 131 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.382 Fit side-chains REVERT: A 31 LYS cc_start: 0.8526 (mppt) cc_final: 0.8285 (mptt) REVERT: A 351 LYS cc_start: 0.7785 (mmmm) cc_final: 0.7449 (mmtt) REVERT: A 783 LEU cc_start: 0.8649 (tp) cc_final: 0.8392 (tp) REVERT: A 830 PHE cc_start: 0.6854 (m-10) cc_final: 0.6573 (m-10) REVERT: A 950 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7975 (tt) REVERT: A 1581 ARG cc_start: 0.7645 (tmt90) cc_final: 0.7339 (tpt-90) outliers start: 25 outliers final: 12 residues processed: 124 average time/residue: 0.4716 time to fit residues: 64.1336 Evaluate side-chains 110 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 337 THR 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 778 ASN 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 7 optimal weight: 0.0770 chunk 86 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 HIS A 434 GLN 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 = 0.3835 r_free = 0.3835 target = 0.157391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.134123 restraints weight = 11225.783| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.64 r_work: 0.3531 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2291 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= 0.309 Angle : 0.749 13.121 14576 Z= 0.364 Chirality : 0.050 0.426 1629 Planarity : 0.005 0.059 1676 Dihedral : 13.290 177.593 1857 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 3.24 % Allowed : 19.76 % 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: -1.21 (0.24), residues: 1154 helix: 0.14 (0.29), residues: 319 sheet: -1.03 (0.35), residues: 195 loop : -1.20 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 472 TYR 0.020 0.002 TYR A1595 PHE 0.022 0.002 PHE A1520 TRP 0.014 0.002 TRP A1685 HIS 0.009 0.002 HIS A 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00720 / 0.31 (10593) covalent geometry : angle 0.70297 / 0.36 (14555) hydrogen bonds : bond 0.04382 / 2.89 ( 346) hydrogen bonds : angle 5.43762 / 3.98 ( 1027) metal coordination : bond 0.01110 / 0.77 ( 16) metal coordination : angle 6.86875 / 4.41 ( 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 126 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 96 time to evaluate : 0.467 Fit side-chains REVERT: A 31 LYS cc_start: 0.8489 (mppt) cc_final: 0.8239 (mptt) REVERT: A 925 TYR cc_start: 0.8104 (m-80) cc_final: 0.7870 (m-80) REVERT: A 950 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8035 (tt) outliers start: 30 outliers final: 15 residues processed: 120 average time/residue: 0.4735 time to fit residues: 62.4890 Evaluate side-chains 101 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 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 514 LEU Chi-restraints excluded: chain A residue 556 THR 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 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: 0.9980 chunk 108 optimal weight: 0.7980 chunk 33 optimal weight: 0.0000 chunk 19 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 434 GLN A 696 ASN ** 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 = 0.3906 r_free = 0.3906 target = 0.164326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.141525 restraints weight = 11115.363| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 1.63 r_work: 0.3618 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10609 Z= 0.154 Angle : 0.621 11.300 14576 Z= 0.310 Chirality : 0.045 0.418 1629 Planarity : 0.005 0.055 1676 Dihedral : 13.161 174.911 1857 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.16 % Allowed : 21.27 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.24), residues: 1154 helix: 0.31 (0.29), residues: 319 sheet: -1.04 (0.34), residues: 195 loop : -1.15 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 467 TYR 0.018 0.001 TYR A1595 PHE 0.016 0.001 PHE A 945 TRP 0.014 0.001 TRP A 612 HIS 0.004 0.001 HIS A 727 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (10593) covalent geometry : angle 0.58953 / 0.31 (14555) hydrogen bonds : bond 0.03892 / 2.65 ( 346) hydrogen bonds : angle 5.17831 / 3.78 ( 1027) metal coordination : bond 0.01187 / 0.82 ( 16) metal coordination : angle 5.18968 / 3.30 ( 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 118 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.398 Fit side-chains REVERT: A 31 LYS cc_start: 0.8576 (mppt) cc_final: 0.8336 (mptt) REVERT: A 783 LEU cc_start: 0.8689 (tp) cc_final: 0.8437 (tp) REVERT: A 830 PHE cc_start: 0.7088 (m-10) cc_final: 0.6887 (m-10) REVERT: A 880 ILE cc_start: 0.6604 (OUTLIER) cc_final: 0.6155 (mt) REVERT: A 925 TYR cc_start: 0.7960 (m-80) cc_final: 0.7753 (m-80) REVERT: A 950 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7883 (tt) outliers start: 20 outliers final: 11 residues processed: 114 average time/residue: 0.4781 time to fit residues: 59.8211 Evaluate side-chains 107 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 556 THR Chi-restraints excluded: chain A residue 678 VAL 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 1507 VAL Chi-restraints excluded: chain A residue 1509 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 77 optimal weight: 0.3980 chunk 87 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 696 ASN ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.163549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.140938 restraints weight = 11047.340| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 1.61 r_work: 0.3606 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10609 Z= 0.172 Angle : 0.635 10.751 14576 Z= 0.315 Chirality : 0.045 0.418 1629 Planarity : 0.005 0.056 1676 Dihedral : 13.096 175.823 1857 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 2.05 % Allowed : 21.60 % Favored : 76.35 % 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: -1.10 (0.24), residues: 1154 helix: 0.35 (0.29), residues: 319 sheet: -0.90 (0.35), residues: 177 loop : -1.23 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 467 TYR 0.023 0.002 TYR A1595 PHE 0.016 0.001 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 0.00395 / 0.17 (10593) covalent geometry : angle 0.60227 / 0.31 (14555) hydrogen bonds : bond 0.03848 / 2.60 ( 346) hydrogen bonds : angle 5.13766 / 3.75 ( 1027) metal coordination : bond 0.00863 / 0.62 ( 16) metal coordination : angle 5.33123 / 3.37 ( 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 114 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.385 Fit side-chains REVERT: A 31 LYS cc_start: 0.8591 (mppt) cc_final: 0.8356 (mptt) REVERT: A 783 LEU cc_start: 0.8701 (tp) cc_final: 0.8455 (tp) REVERT: A 830 PHE cc_start: 0.7091 (m-10) cc_final: 0.6874 (m-10) REVERT: A 925 TYR cc_start: 0.7992 (m-80) cc_final: 0.7788 (m-80) REVERT: A 950 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7947 (tt) outliers start: 19 outliers final: 13 residues processed: 110 average time/residue: 0.5065 time to fit residues: 60.8452 Evaluate side-chains 103 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 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 556 THR 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 950 LEU Chi-restraints excluded: chain A residue 1507 VAL Chi-restraints excluded: chain A residue 1509 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 54 optimal weight: 0.0980 chunk 75 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 103 optimal weight: 0.0970 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 696 ASN ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.164070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.141355 restraints weight = 11219.426| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 1.63 r_work: 0.3612 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10609 Z= 0.167 Angle : 0.630 10.845 14576 Z= 0.312 Chirality : 0.045 0.417 1629 Planarity : 0.005 0.055 1676 Dihedral : 13.071 175.560 1857 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 2.27 % Allowed : 21.71 % Favored : 76.03 % 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: -1.10 (0.24), residues: 1154 helix: 0.36 (0.29), residues: 321 sheet: -0.87 (0.35), residues: 177 loop : -1.25 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 467 TYR 0.021 0.002 TYR A1595 PHE 0.015 0.001 PHE A 945 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 0.00384 / 0.17 (10593) covalent geometry : angle 0.59781 / 0.31 (14555) hydrogen bonds : bond 0.03827 / 2.59 ( 346) hydrogen bonds : angle 5.10796 / 3.73 ( 1027) metal coordination : bond 0.00881 / 0.65 ( 16) metal coordination : angle 5.23932 / 3.31 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3264.33 seconds wall clock time: 56 minutes 46.93 seconds (3406.93 seconds total)