Starting phenix.real_space_refine on Sat Aug 23 07:37:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gna_34158/08_2025/8gna_34158.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gna_34158/08_2025/8gna_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_2025/8gna_34158.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gna_34158/08_2025/8gna_34158.map" model { file = "/net/cci-nas-00/data/ceres_data/8gna_34158/08_2025/8gna_34158.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gna_34158/08_2025/8gna_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-2.0-5787/lib/python3.9/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: 2.77, 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: 0.95 Conformation dependent library (CDL) restraints added in 521.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.55 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: 2.54 Time building geometry restraints manager: 1.27 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: 6096 35.29 - 70.58: 215 70.58 - 105.87: 19 105.87 - 141.17: 2 141.17 - 176.46: 2 Dihedral angle restraints: 6334 sinusoidal: 2950 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 6331 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: 2.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.700 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: 0.010 Load rotamer database and sin/cos tables:8.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 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 : 17.064 176.458 4160 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 aren 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 covalent geometry : bond 0.00255 (10593) covalent geometry : angle 0.57587 (14555) hydrogen bonds : bond 0.22501 ( 346) hydrogen bonds : angle 9.07327 ( 1027) metal coordination : bond 0.01176 ( 16) metal coordination : angle 5.11837 ( 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 : 0.437 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.5952 time to fit residues: 100.0523 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 : 0.437 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 109 HIS ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 ASN A 696 ASN ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1516 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.163075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.140363 restraints weight = 11048.234| |-----------------------------------------------------------------------------| 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: 0.3481 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10609 Z= 0.219 Angle : 0.688 16.122 14576 Z= 0.338 Chirality : 0.046 0.379 1629 Planarity : 0.005 0.052 1676 Dihedral : 17.465 176.788 2029 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 2.05 % Allowed : 11.34 % Favored : 86.61 % 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 aren not related in a simple way. whole: -0.92 (0.24), residues: 1154 helix: 0.29 (0.29), residues: 312 sheet: -0.44 (0.39), residues: 172 loop : -1.09 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 467 TYR 0.019 0.002 TYR A1595 PHE 0.018 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 covalent geometry : bond 0.00498 (10593) covalent geometry : angle 0.63895 (14555) hydrogen bonds : bond 0.05302 ( 346) hydrogen bonds : angle 6.14660 ( 1027) metal coordination : bond 0.01010 ( 16) metal coordination : angle 6.76228 ( 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 : 0.391 Fit side-chains REVERT: A 498 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7445 (mp-120) REVERT: A 611 GLU cc_start: 0.8685 (pt0) cc_final: 0.8452 (pt0) REVERT: A 717 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7651 (mt-10) REVERT: A 925 TYR cc_start: 0.8002 (m-80) cc_final: 0.7789 (m-80) REVERT: A 1595 TYR cc_start: 0.8342 (t80) cc_final: 0.8125 (t80) outliers start: 19 outliers final: 6 residues processed: 128 average time/residue: 0.5889 time to fit residues: 81.3406 Evaluate side-chains 103 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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: 0.7980 chunk 32 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 65 optimal weight: 0.0010 chunk 90 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 ASN A 696 ASN A 786 HIS ** 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 = 0.3866 r_free = 0.3866 target = 0.160692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.137847 restraints weight = 11182.875| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.62 r_work: 0.3574 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10609 Z= 0.222 Angle : 0.674 15.183 14576 Z= 0.332 Chirality : 0.046 0.410 1629 Planarity : 0.005 0.052 1676 Dihedral : 17.487 176.331 2029 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.78 % Allowed : 13.50 % Favored : 82.72 % 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 aren not related in a simple way. whole: -1.04 (0.24), residues: 1154 helix: 0.23 (0.29), residues: 318 sheet: -0.67 (0.37), residues: 174 loop : -1.16 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 472 TYR 0.012 0.002 TYR A 922 PHE 0.016 0.002 PHE A 284 TRP 0.012 0.002 TRP A 82 HIS 0.008 0.001 HIS A 455 Details of bonding type rmsd covalent geometry : bond 0.00510 (10593) covalent geometry : angle 0.62831 (14555) hydrogen bonds : bond 0.04532 ( 346) hydrogen bonds : angle 5.68571 ( 1027) metal coordination : bond 0.01036 ( 16) metal coordination : angle 6.43913 ( 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 146 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 111 time to evaluate : 0.388 Fit side-chains REVERT: A 36 MET cc_start: 0.8822 (mmm) cc_final: 0.8589 (mmt) REVERT: A 93 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.6530 (mp10) REVERT: A 498 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7351 (mp-120) REVERT: A 611 GLU cc_start: 0.8628 (pt0) cc_final: 0.8334 (pt0) REVERT: A 622 ILE cc_start: 0.7647 (OUTLIER) cc_final: 0.7440 (mp) REVERT: A 717 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7656 (mt-10) REVERT: A 830 PHE cc_start: 0.7348 (m-10) cc_final: 0.7096 (m-10) REVERT: A 1435 LYS cc_start: 0.8323 (ptpp) cc_final: 0.7910 (ptmm) outliers start: 35 outliers final: 15 residues processed: 136 average time/residue: 0.5445 time to fit residues: 80.0646 Evaluate side-chains 107 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 93 GLN 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 493 VAL Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 622 ILE 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 880 ILE 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: 2.9990 chunk 96 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 88 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3885 r_free = 0.3885 target = 0.162417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.139730 restraints weight = 11203.463| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.62 r_work: 0.3593 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10609 Z= 0.178 Angle : 0.635 12.933 14576 Z= 0.317 Chirality : 0.045 0.413 1629 Planarity : 0.005 0.050 1676 Dihedral : 17.466 175.703 2029 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.67 % Allowed : 15.55 % Favored : 80.78 % 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 aren not related in a simple way. whole: -1.08 (0.24), residues: 1154 helix: 0.24 (0.29), residues: 320 sheet: -0.89 (0.35), residues: 195 loop : -1.14 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 467 TYR 0.021 0.001 TYR A1595 PHE 0.014 0.001 PHE A1520 TRP 0.012 0.001 TRP A 612 HIS 0.005 0.001 HIS A 455 Details of bonding type rmsd covalent geometry : bond 0.00407 (10593) covalent geometry : angle 0.59600 (14555) hydrogen bonds : bond 0.04191 ( 346) hydrogen bonds : angle 5.47839 ( 1027) metal coordination : bond 0.00926 ( 16) metal coordination : angle 5.80939 ( 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: 34 poor density : 100 time to evaluate : 0.382 Fit side-chains REVERT: A 498 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7296 (mp-120) REVERT: A 615 ASN cc_start: 0.7617 (t0) cc_final: 0.7299 (t0) REVERT: A 717 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7683 (mt-10) REVERT: A 830 PHE cc_start: 0.7195 (m-10) cc_final: 0.6980 (m-10) outliers start: 34 outliers final: 16 residues processed: 124 average time/residue: 0.5622 time to fit residues: 75.3982 Evaluate side-chains 107 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 237 ILE 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 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 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: 0.6980 chunk 77 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3882 r_free = 0.3882 target = 0.162103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.139398 restraints weight = 11165.916| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 1.62 r_work: 0.3589 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10609 Z= 0.189 Angle : 0.638 12.417 14576 Z= 0.317 Chirality : 0.046 0.427 1629 Planarity : 0.005 0.051 1676 Dihedral : 17.414 175.750 2029 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 3.35 % Allowed : 17.17 % 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 aren not related in a simple way. whole: -1.10 (0.24), residues: 1154 helix: 0.26 (0.29), residues: 319 sheet: -0.94 (0.35), residues: 195 loop : -1.15 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 719 TYR 0.022 0.001 TYR A1595 PHE 0.015 0.001 PHE A1520 TRP 0.014 0.001 TRP A 612 HIS 0.006 0.001 HIS A 455 Details of bonding type rmsd covalent geometry : bond 0.00433 (10593) covalent geometry : angle 0.59951 (14555) hydrogen bonds : bond 0.04163 ( 346) hydrogen bonds : angle 5.37223 ( 1027) metal coordination : bond 0.00889 ( 16) metal coordination : angle 5.75018 ( 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 137 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 106 time to evaluate : 0.395 Fit side-chains REVERT: A 498 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7224 (mp-120) REVERT: A 567 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7819 (tttp) REVERT: A 615 ASN cc_start: 0.7661 (t0) cc_final: 0.7318 (t0) REVERT: A 717 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7708 (mt-10) REVERT: A 830 PHE cc_start: 0.7087 (m-10) cc_final: 0.6883 (m-10) REVERT: A 925 TYR cc_start: 0.7983 (m-80) cc_final: 0.7775 (m-80) REVERT: A 950 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7987 (tt) outliers start: 31 outliers final: 17 residues processed: 129 average time/residue: 0.5693 time to fit residues: 79.3169 Evaluate side-chains 113 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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 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 567 LYS 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 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: 2.9990 chunk 90 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 120 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 76 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS ** A 179 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.164666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.142058 restraints weight = 11219.157| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.63 r_work: 0.3619 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2074 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= 0.152 Angle : 0.607 11.026 14576 Z= 0.304 Chirality : 0.044 0.425 1629 Planarity : 0.004 0.051 1676 Dihedral : 17.341 175.129 2029 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 3.89 % Allowed : 17.17 % Favored : 78.94 % 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 aren not related in a simple way. whole: -0.97 (0.24), residues: 1154 helix: 0.41 (0.29), residues: 319 sheet: -0.92 (0.35), residues: 195 loop : -1.09 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 467 TYR 0.019 0.001 TYR A1595 PHE 0.013 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 covalent geometry : bond 0.00346 (10593) covalent geometry : angle 0.57673 (14555) hydrogen bonds : bond 0.04010 ( 346) hydrogen bonds : angle 5.21190 ( 1027) metal coordination : bond 0.00967 ( 16) metal coordination : angle 5.05578 ( 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 147 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 111 time to evaluate : 0.449 Fit side-chains REVERT: A 615 ASN cc_start: 0.7740 (t0) cc_final: 0.7475 (t0) REVERT: A 830 PHE cc_start: 0.6908 (OUTLIER) cc_final: 0.6587 (m-10) REVERT: A 925 TYR cc_start: 0.7945 (m-80) cc_final: 0.7712 (m-80) outliers start: 36 outliers final: 16 residues processed: 137 average time/residue: 0.5311 time to fit residues: 79.2475 Evaluate side-chains 112 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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 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 830 PHE Chi-restraints excluded: chain A residue 880 ILE 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: 0.0870 chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 65 optimal weight: 0.0010 chunk 95 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.165293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.142651 restraints weight = 11056.309| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 1.62 r_work: 0.3613 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10609 Z= 0.150 Angle : 0.600 10.368 14576 Z= 0.302 Chirality : 0.044 0.424 1629 Planarity : 0.004 0.050 1676 Dihedral : 17.275 175.053 2029 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.35 % Allowed : 18.68 % Favored : 77.97 % 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 aren not related in a simple way. whole: -0.94 (0.24), residues: 1154 helix: 0.48 (0.29), residues: 320 sheet: -0.84 (0.36), residues: 177 loop : -1.13 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 467 TYR 0.017 0.001 TYR A1595 PHE 0.014 0.001 PHE A1520 TRP 0.013 0.001 TRP A 612 HIS 0.004 0.001 HIS A 727 Details of bonding type rmsd covalent geometry : bond 0.00341 (10593) covalent geometry : angle 0.57030 (14555) hydrogen bonds : bond 0.03877 ( 346) hydrogen bonds : angle 5.11915 ( 1027) metal coordination : bond 0.00888 ( 16) metal coordination : angle 4.91936 ( 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 134 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 0.359 Fit side-chains REVERT: A 31 LYS cc_start: 0.8561 (mppt) cc_final: 0.8339 (mptt) REVERT: A 615 ASN cc_start: 0.7734 (t0) cc_final: 0.7472 (t0) REVERT: A 830 PHE cc_start: 0.6800 (OUTLIER) cc_final: 0.6481 (m-10) REVERT: A 925 TYR cc_start: 0.7970 (m-80) cc_final: 0.7711 (m-80) REVERT: A 1581 ARG cc_start: 0.7686 (tmt90) cc_final: 0.7409 (tpt-90) outliers start: 31 outliers final: 15 residues processed: 127 average time/residue: 0.5301 time to fit residues: 73.1702 Evaluate side-chains 108 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 101 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 56 optimal weight: 8.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3815 r_free = 0.3815 target = 0.155469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.132277 restraints weight = 11245.200| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.65 r_work: 0.3508 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.056 10609 Z= 0.374 Angle : 0.809 14.098 14576 Z= 0.391 Chirality : 0.053 0.433 1629 Planarity : 0.006 0.058 1676 Dihedral : 17.543 176.288 2029 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 4.10 % Allowed : 19.01 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.24), residues: 1154 helix: 0.05 (0.28), residues: 320 sheet: -1.10 (0.35), residues: 195 loop : -1.29 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 472 TYR 0.021 0.003 TYR A1595 PHE 0.024 0.002 PHE A1520 TRP 0.018 0.002 TRP A1685 HIS 0.011 0.002 HIS A 455 Details of bonding type rmsd covalent geometry : bond 0.00875 (10593) covalent geometry : angle 0.75947 (14555) hydrogen bonds : bond 0.04652 ( 346) hydrogen bonds : angle 5.56998 ( 1027) metal coordination : bond 0.01239 ( 16) metal coordination : angle 7.35962 ( 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 127 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 89 time to evaluate : 0.387 Fit side-chains REVERT: A 31 LYS cc_start: 0.8509 (mppt) cc_final: 0.8257 (mptt) REVERT: A 498 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7223 (mp-120) REVERT: A 567 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.7988 (tttp) REVERT: A 591 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8627 (mt) REVERT: A 615 ASN cc_start: 0.7734 (t0) cc_final: 0.7435 (t0) REVERT: A 830 PHE cc_start: 0.7282 (OUTLIER) cc_final: 0.7075 (m-10) REVERT: A 950 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8043 (tt) outliers start: 38 outliers final: 17 residues processed: 120 average time/residue: 0.5115 time to fit residues: 67.1108 Evaluate side-chains 104 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 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 514 LEU Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 567 LYS Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 778 ASN Chi-restraints excluded: chain A residue 830 PHE 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: 0.7980 chunk 19 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 chunk 99 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.163454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.140774 restraints weight = 11137.584| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 1.63 r_work: 0.3609 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10609 Z= 0.156 Angle : 0.628 11.749 14576 Z= 0.314 Chirality : 0.045 0.418 1629 Planarity : 0.005 0.059 1676 Dihedral : 17.398 173.395 2029 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.59 % Allowed : 20.84 % 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 aren not related in a simple way. whole: -1.13 (0.24), residues: 1154 helix: 0.35 (0.29), residues: 319 sheet: -1.05 (0.34), residues: 195 loop : -1.21 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 467 TYR 0.015 0.001 TYR A1595 PHE 0.014 0.001 PHE A1520 TRP 0.013 0.001 TRP A 612 HIS 0.005 0.001 HIS A 727 Details of bonding type rmsd covalent geometry : bond 0.00351 (10593) covalent geometry : angle 0.59480 (14555) hydrogen bonds : bond 0.03988 ( 346) hydrogen bonds : angle 5.23087 ( 1027) metal coordination : bond 0.01134 ( 16) metal coordination : angle 5.34377 ( 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 117 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.367 Fit side-chains REVERT: A 31 LYS cc_start: 0.8516 (mppt) cc_final: 0.8284 (mptt) REVERT: A 615 ASN cc_start: 0.7686 (t0) cc_final: 0.7410 (t0) REVERT: A 830 PHE cc_start: 0.6918 (OUTLIER) cc_final: 0.6641 (m-10) REVERT: A 925 TYR cc_start: 0.7981 (m-80) cc_final: 0.7764 (m-80) outliers start: 24 outliers final: 15 residues processed: 113 average time/residue: 0.4987 time to fit residues: 61.7513 Evaluate side-chains 107 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 505 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 830 PHE 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: 1.9990 chunk 63 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.164345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.141708 restraints weight = 11037.184| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 1.62 r_work: 0.3620 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10609 Z= 0.151 Angle : 0.616 10.465 14576 Z= 0.308 Chirality : 0.044 0.416 1629 Planarity : 0.004 0.055 1676 Dihedral : 17.287 174.540 2029 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 2.05 % Allowed : 21.92 % 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 aren not related in a simple way. whole: -1.06 (0.24), residues: 1154 helix: 0.42 (0.29), residues: 320 sheet: -0.89 (0.35), residues: 177 loop : -1.22 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 467 TYR 0.023 0.002 TYR A1595 PHE 0.014 0.001 PHE A1520 TRP 0.011 0.001 TRP A 612 HIS 0.004 0.001 HIS A 727 Details of bonding type rmsd covalent geometry : bond 0.00344 (10593) covalent geometry : angle 0.58528 (14555) hydrogen bonds : bond 0.03834 ( 346) hydrogen bonds : angle 5.11299 ( 1027) metal coordination : bond 0.00865 ( 16) metal coordination : angle 5.06267 ( 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 117 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.390 Fit side-chains REVERT: A 31 LYS cc_start: 0.8588 (mppt) cc_final: 0.8357 (mptt) REVERT: A 357 LYS cc_start: 0.7687 (mptp) cc_final: 0.7310 (ttmm) REVERT: A 615 ASN cc_start: 0.7661 (t0) cc_final: 0.7392 (t0) REVERT: A 830 PHE cc_start: 0.6818 (OUTLIER) cc_final: 0.6530 (m-10) REVERT: A 925 TYR cc_start: 0.8014 (m-80) cc_final: 0.7797 (m-80) REVERT: A 950 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7898 (tt) REVERT: A 1581 ARG cc_start: 0.7725 (tmt90) cc_final: 0.7439 (tpt-90) outliers start: 19 outliers final: 14 residues processed: 113 average time/residue: 0.5572 time to fit residues: 68.3793 Evaluate side-chains 107 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 505 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 830 PHE 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: 1.9990 chunk 75 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 94 optimal weight: 0.0670 chunk 103 optimal weight: 0.5980 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.164880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.142129 restraints weight = 11211.708| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 1.63 r_work: 0.3612 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10609 Z= 0.152 Angle : 0.610 10.045 14576 Z= 0.306 Chirality : 0.044 0.416 1629 Planarity : 0.005 0.055 1676 Dihedral : 17.239 174.187 2029 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.38 % Allowed : 21.60 % 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 aren not related in a simple way. whole: -1.03 (0.24), residues: 1154 helix: 0.45 (0.29), residues: 322 sheet: -0.82 (0.36), residues: 177 loop : -1.24 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 467 TYR 0.023 0.002 TYR A1595 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 covalent geometry : bond 0.00346 (10593) covalent geometry : angle 0.58005 (14555) hydrogen bonds : bond 0.03829 ( 346) hydrogen bonds : angle 5.05547 ( 1027) metal coordination : bond 0.00906 ( 16) metal coordination : angle 5.01280 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3423.36 seconds wall clock time: 59 minutes 29.45 seconds (3569.45 seconds total)