Starting phenix.real_space_refine on Mon Jul 28 19:15:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gna_34158/07_2025/8gna_34158.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gna_34158/07_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_34158/07_2025/8gna_34158.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gna_34158/07_2025/8gna_34158.map" model { file = "/net/cci-nas-00/data/ceres_data/8gna_34158/07_2025/8gna_34158.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gna_34158/07_2025/8gna_34158.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 5, 'ASN:plan1': 12, 'ASP:plan': 23, 'PHE:plan': 1, 'GLU:plan': 31, 'ARG:plan': 6} 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: 7.09, per 1000 atoms: 0.69 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: 2.60 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 4.46 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: 5.97 Time building geometry restraints manager: 3.08 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: 41.340 Set stop_for_unknowns flag: 0.010 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 35.600 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:14.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.510 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (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 TRP 0.011 0.001 TRP A 82 HIS 0.003 0.001 HIS A1621 PHE 0.017 0.001 PHE A 284 TYR 0.012 0.001 TYR A1590 ARG 0.003 0.000 ARG A 212 Details of bonding type rmsd hydrogen bonds : bond 0.22501 ( 346) hydrogen bonds : angle 9.07327 ( 1027) metal coordination : bond 0.01176 ( 16) metal coordination : angle 5.11837 ( 21) covalent geometry : bond 0.00255 (10593) covalent geometry : angle 0.57587 (14555) *********************** 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 : 1.281 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 1.3172 time to fit residues: 222.5601 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 : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.9980 chunk 92 optimal weight: 0.0870 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 62 optimal weight: 0.4980 chunk 49 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 overall best weight: 0.8960 ------------------------------------------------------------------------------- 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 ** 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 = 0.3912 r_free = 0.3912 target = 0.164639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.142105 restraints weight = 11052.869| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 1.61 r_work: 0.3620 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10609 Z= 0.194 Angle : 0.671 15.907 14576 Z= 0.331 Chirality : 0.046 0.381 1629 Planarity : 0.005 0.051 1676 Dihedral : 17.435 176.446 2029 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.05 % Allowed : 11.66 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.24), residues: 1154 helix: 0.34 (0.29), residues: 313 sheet: -0.44 (0.40), residues: 162 loop : -1.04 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 82 HIS 0.005 0.001 HIS A 455 PHE 0.018 0.002 PHE A 284 TYR 0.020 0.002 TYR A1595 ARG 0.005 0.001 ARG A 472 Details of bonding type rmsd hydrogen bonds : bond 0.04876 ( 346) hydrogen bonds : angle 6.04863 ( 1027) metal coordination : bond 0.01227 ( 16) metal coordination : angle 6.46988 ( 21) covalent geometry : bond 0.00438 (10593) covalent geometry : angle 0.62479 (14555) *********************** 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 136 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.974 Fit side-chains REVERT: A 351 LYS cc_start: 0.7781 (mmmm) cc_final: 0.7454 (mmtt) REVERT: A 415 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7629 (tt0) REVERT: A 498 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7449 (mp-120) REVERT: A 611 GLU cc_start: 0.8628 (pt0) cc_final: 0.8385 (pt0) REVERT: A 717 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7656 (mt-10) REVERT: A 1595 TYR cc_start: 0.8304 (t80) cc_final: 0.8086 (t80) outliers start: 19 outliers final: 6 residues processed: 130 average time/residue: 1.1966 time to fit residues: 168.8518 Evaluate side-chains 109 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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 415 GLU Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 1509 THR Chi-restraints excluded: chain A residue 1639 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 119 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 49 optimal weight: 0.1980 chunk 80 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 109 HIS A 696 ASN ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.165206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.142628 restraints weight = 11188.202| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 1.62 r_work: 0.3627 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1683 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= 0.159 Angle : 0.611 13.004 14576 Z= 0.306 Chirality : 0.044 0.402 1629 Planarity : 0.004 0.049 1676 Dihedral : 17.390 175.517 2029 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.92 % Allowed : 13.28 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.24), residues: 1154 helix: 0.48 (0.30), residues: 314 sheet: -0.53 (0.38), residues: 166 loop : -1.05 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 82 HIS 0.005 0.001 HIS A 455 PHE 0.013 0.001 PHE A 284 TYR 0.012 0.001 TYR A1595 ARG 0.005 0.000 ARG A1505 Details of bonding type rmsd hydrogen bonds : bond 0.04393 ( 346) hydrogen bonds : angle 5.55194 ( 1027) metal coordination : bond 0.01069 ( 16) metal coordination : angle 5.48542 ( 21) covalent geometry : bond 0.00360 (10593) covalent geometry : angle 0.57529 (14555) *********************** 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: 27 poor density : 115 time to evaluate : 1.077 Fit side-chains REVERT: A 351 LYS cc_start: 0.7805 (mmmm) cc_final: 0.7473 (mmtt) REVERT: A 498 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7359 (mp-120) REVERT: A 622 ILE cc_start: 0.7456 (mp) cc_final: 0.7253 (mp) REVERT: A 717 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7628 (mt-10) REVERT: A 830 PHE cc_start: 0.7190 (m-10) cc_final: 0.6921 (m-10) REVERT: A 1435 LYS cc_start: 0.8219 (ptpp) cc_final: 0.7309 (mttt) outliers start: 27 outliers final: 10 residues processed: 134 average time/residue: 1.2100 time to fit residues: 176.2145 Evaluate side-chains 105 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 678 VAL 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 20 optimal weight: 2.9990 chunk 6 optimal weight: 0.3980 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS 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 = 0.3879 r_free = 0.3879 target = 0.162086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.139387 restraints weight = 11024.072| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.61 r_work: 0.3591 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 10609 Z= 0.204 Angle : 0.648 12.811 14576 Z= 0.321 Chirality : 0.046 0.421 1629 Planarity : 0.005 0.050 1676 Dihedral : 17.361 176.189 2029 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 3.67 % Allowed : 15.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.24), residues: 1154 helix: 0.31 (0.29), residues: 320 sheet: -0.89 (0.35), residues: 195 loop : -1.09 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 612 HIS 0.007 0.001 HIS A 455 PHE 0.016 0.002 PHE A1520 TYR 0.018 0.002 TYR A1595 ARG 0.004 0.001 ARG A 472 Details of bonding type rmsd hydrogen bonds : bond 0.04208 ( 346) hydrogen bonds : angle 5.42328 ( 1027) metal coordination : bond 0.00891 ( 16) metal coordination : angle 5.93138 ( 21) covalent geometry : bond 0.00469 (10593) covalent geometry : angle 0.60777 (14555) *********************** 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 141 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 1.047 Fit side-chains REVERT: A 498 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7302 (mp-120) REVERT: A 717 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7665 (mt-10) REVERT: A 830 PHE cc_start: 0.7180 (m-10) cc_final: 0.6971 (m-10) REVERT: A 950 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8023 (tt) REVERT: A 1435 LYS cc_start: 0.8281 (ptpp) cc_final: 0.7875 (ptmm) outliers start: 34 outliers final: 14 residues processed: 131 average time/residue: 1.1311 time to fit residues: 161.1606 Evaluate side-chains 113 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 204 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 675 THR Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 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 34 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3905 r_free = 0.3905 target = 0.164170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.141580 restraints weight = 11039.284| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 1.61 r_work: 0.3613 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10609 Z= 0.165 Angle : 0.613 11.711 14576 Z= 0.307 Chirality : 0.045 0.418 1629 Planarity : 0.004 0.049 1676 Dihedral : 17.324 175.479 2029 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 3.46 % Allowed : 16.31 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.24), residues: 1154 helix: 0.40 (0.29), residues: 319 sheet: -0.94 (0.35), residues: 195 loop : -1.10 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 612 HIS 0.004 0.001 HIS A 455 PHE 0.014 0.001 PHE A1520 TYR 0.019 0.001 TYR A1595 ARG 0.005 0.000 ARG A 467 Details of bonding type rmsd hydrogen bonds : bond 0.04088 ( 346) hydrogen bonds : angle 5.27616 ( 1027) metal coordination : bond 0.00898 ( 16) metal coordination : angle 5.37000 ( 21) covalent geometry : bond 0.00378 (10593) covalent geometry : angle 0.57883 (14555) *********************** 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 144 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 1.190 Fit side-chains REVERT: A 717 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7699 (mt-10) REVERT: A 830 PHE cc_start: 0.6979 (m-10) cc_final: 0.6751 (m-10) REVERT: A 950 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7981 (tt) outliers start: 32 outliers final: 16 residues processed: 135 average time/residue: 1.0865 time to fit residues: 160.2901 Evaluate side-chains 111 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 1.188 ------------------------------------------------------------------------------- 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 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 675 THR Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 778 ASN Chi-restraints excluded: chain A residue 880 ILE Chi-restraints excluded: chain A residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS A 434 GLN A 502 ASN A 696 ASN ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.163945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.141176 restraints weight = 11169.722| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 1.63 r_work: 0.3612 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2065 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= 0.166 Angle : 0.621 11.302 14576 Z= 0.309 Chirality : 0.045 0.419 1629 Planarity : 0.004 0.049 1676 Dihedral : 17.291 175.540 2029 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 3.89 % Allowed : 17.49 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.24), residues: 1154 helix: 0.43 (0.29), residues: 319 sheet: -0.96 (0.35), residues: 195 loop : -1.08 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 612 HIS 0.005 0.001 HIS A 455 PHE 0.014 0.001 PHE A1520 TYR 0.020 0.001 TYR A1595 ARG 0.005 0.000 ARG A 467 Details of bonding type rmsd hydrogen bonds : bond 0.03982 ( 346) hydrogen bonds : angle 5.19501 ( 1027) metal coordination : bond 0.00853 ( 16) metal coordination : angle 5.26188 ( 21) covalent geometry : bond 0.00380 (10593) covalent geometry : angle 0.58832 (14555) *********************** 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 145 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 109 time to evaluate : 1.023 Fit side-chains REVERT: A 31 LYS cc_start: 0.8555 (mppt) cc_final: 0.8346 (mptt) REVERT: A 194 THR cc_start: 0.8153 (OUTLIER) cc_final: 0.7939 (p) REVERT: A 498 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7285 (mp-120) REVERT: A 783 LEU cc_start: 0.8666 (tp) cc_final: 0.8431 (tp) REVERT: A 830 PHE cc_start: 0.6926 (m-10) cc_final: 0.6651 (m-10) REVERT: A 925 TYR cc_start: 0.7969 (m-80) cc_final: 0.7752 (m-80) REVERT: A 950 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.8016 (tt) REVERT: A 1435 LYS cc_start: 0.8233 (ptpp) cc_final: 0.7334 (mttt) outliers start: 36 outliers final: 19 residues processed: 134 average time/residue: 1.0359 time to fit residues: 151.8736 Evaluate side-chains 121 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 201 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 675 THR Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 684 THR 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 94 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 20 optimal weight: 0.0980 chunk 111 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 chunk 118 optimal weight: 4.9990 chunk 65 optimal weight: 0.1980 chunk 41 optimal weight: 0.0030 chunk 28 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 overall best weight: 0.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 109 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.169550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.147245 restraints weight = 11204.049| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 1.61 r_work: 0.3667 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10609 Z= 0.118 Angle : 0.568 8.874 14576 Z= 0.290 Chirality : 0.043 0.423 1629 Planarity : 0.004 0.047 1676 Dihedral : 17.169 174.322 2029 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.92 % Allowed : 19.01 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.24), residues: 1154 helix: 0.71 (0.30), residues: 316 sheet: -0.95 (0.35), residues: 185 loop : -1.02 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 612 HIS 0.004 0.001 HIS A 727 PHE 0.010 0.001 PHE A1520 TYR 0.010 0.001 TYR A1595 ARG 0.003 0.000 ARG A 168 Details of bonding type rmsd hydrogen bonds : bond 0.03959 ( 346) hydrogen bonds : angle 4.98107 ( 1027) metal coordination : bond 0.01127 ( 16) metal coordination : angle 4.22605 ( 21) covalent geometry : bond 0.00260 (10593) covalent geometry : angle 0.54534 (14555) *********************** 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 148 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 1.090 Fit side-chains REVERT: A 357 LYS cc_start: 0.7709 (mptp) cc_final: 0.7290 (ttmm) REVERT: A 783 LEU cc_start: 0.8546 (tp) cc_final: 0.8306 (tp) REVERT: A 925 TYR cc_start: 0.7880 (m-80) cc_final: 0.7674 (m-80) REVERT: A 950 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7959 (tt) REVERT: A 1435 LYS cc_start: 0.8032 (ptpp) cc_final: 0.7491 (ptpt) outliers start: 27 outliers final: 11 residues processed: 139 average time/residue: 1.0188 time to fit residues: 156.4747 Evaluate side-chains 116 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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 675 THR Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 950 LEU 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 68 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 41 optimal weight: 0.0670 chunk 109 optimal weight: 0.0020 chunk 110 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.6128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** 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 = 0.3926 r_free = 0.3926 target = 0.166339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.143652 restraints weight = 11171.338| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 1.63 r_work: 0.3631 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3511 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2201 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= 0.147 Angle : 0.593 9.485 14576 Z= 0.298 Chirality : 0.044 0.421 1629 Planarity : 0.004 0.047 1676 Dihedral : 17.141 175.068 2029 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.81 % Allowed : 19.87 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.24), residues: 1154 helix: 0.72 (0.30), residues: 316 sheet: -0.88 (0.35), residues: 181 loop : -1.03 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 612 HIS 0.004 0.001 HIS A 727 PHE 0.013 0.001 PHE A1520 TYR 0.014 0.001 TYR A1595 ARG 0.004 0.000 ARG A 467 Details of bonding type rmsd hydrogen bonds : bond 0.03785 ( 346) hydrogen bonds : angle 4.95692 ( 1027) metal coordination : bond 0.00775 ( 16) metal coordination : angle 4.67837 ( 21) covalent geometry : bond 0.00336 (10593) covalent geometry : angle 0.56652 (14555) *********************** 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 137 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 1.150 Fit side-chains REVERT: A 351 LYS cc_start: 0.7795 (mmmm) cc_final: 0.7474 (mmtt) REVERT: A 783 LEU cc_start: 0.8559 (tp) cc_final: 0.8343 (tp) REVERT: A 830 PHE cc_start: 0.6645 (OUTLIER) cc_final: 0.6372 (m-10) REVERT: A 925 TYR cc_start: 0.7959 (m-80) cc_final: 0.7726 (m-80) REVERT: A 950 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.8028 (tt) REVERT: A 1435 LYS cc_start: 0.8107 (ptpp) cc_final: 0.7553 (ptpt) outliers start: 26 outliers final: 13 residues processed: 129 average time/residue: 1.0740 time to fit residues: 152.0285 Evaluate side-chains 118 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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 675 THR Chi-restraints excluded: chain A residue 678 VAL 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 120 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 98 optimal weight: 0.5980 chunk 16 optimal weight: 0.2980 chunk 106 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 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 = 0.3931 r_free = 0.3931 target = 0.166746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.143927 restraints weight = 11201.701| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 1.64 r_work: 0.3633 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2243 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= 0.143 Angle : 0.594 9.349 14576 Z= 0.298 Chirality : 0.044 0.421 1629 Planarity : 0.004 0.048 1676 Dihedral : 17.133 174.638 2029 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.48 % Allowed : 19.98 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.24), residues: 1154 helix: 0.71 (0.30), residues: 316 sheet: -0.91 (0.34), residues: 185 loop : -1.04 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 612 HIS 0.004 0.001 HIS A 727 PHE 0.014 0.001 PHE A 15 TYR 0.014 0.001 TYR A1595 ARG 0.005 0.000 ARG A 467 Details of bonding type rmsd hydrogen bonds : bond 0.03825 ( 346) hydrogen bonds : angle 4.93595 ( 1027) metal coordination : bond 0.00856 ( 16) metal coordination : angle 4.61870 ( 21) covalent geometry : bond 0.00326 (10593) covalent geometry : angle 0.56783 (14555) *********************** 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 126 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 1.172 Fit side-chains REVERT: A 351 LYS cc_start: 0.7804 (mmmm) cc_final: 0.7507 (mmtt) REVERT: A 357 LYS cc_start: 0.7702 (mptp) cc_final: 0.7340 (ttmm) REVERT: A 783 LEU cc_start: 0.8552 (tp) cc_final: 0.8347 (tp) REVERT: A 950 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.8020 (tt) REVERT: A 1435 LYS cc_start: 0.8105 (ptpp) cc_final: 0.7261 (mttt) outliers start: 23 outliers final: 14 residues processed: 119 average time/residue: 1.1104 time to fit residues: 144.6467 Evaluate side-chains 116 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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 675 THR Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 880 ILE Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 1507 VAL Chi-restraints excluded: chain A residue 1509 THR Chi-restraints excluded: chain A residue 1511 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 1 optimal weight: 1.9990 chunk 60 optimal weight: 0.0970 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 102 optimal weight: 0.0370 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 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 = 0.3953 r_free = 0.3953 target = 0.168837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.146152 restraints weight = 11139.186| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.63 r_work: 0.3657 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2331 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= 0.128 Angle : 0.585 8.949 14576 Z= 0.295 Chirality : 0.043 0.421 1629 Planarity : 0.004 0.049 1676 Dihedral : 17.063 174.617 2029 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.16 % Allowed : 20.41 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.24), residues: 1154 helix: 0.76 (0.30), residues: 316 sheet: -0.99 (0.34), residues: 186 loop : -1.04 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 612 HIS 0.004 0.001 HIS A 727 PHE 0.012 0.001 PHE A1520 TYR 0.013 0.001 TYR A1595 ARG 0.005 0.000 ARG A 467 Details of bonding type rmsd hydrogen bonds : bond 0.03814 ( 346) hydrogen bonds : angle 4.86322 ( 1027) metal coordination : bond 0.00900 ( 16) metal coordination : angle 4.34499 ( 21) covalent geometry : bond 0.00289 (10593) covalent geometry : angle 0.56123 (14555) ********************** 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 129 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 1.099 Fit side-chains REVERT: A 357 LYS cc_start: 0.7710 (mptp) cc_final: 0.7350 (ttmm) REVERT: A 783 LEU cc_start: 0.8512 (tp) cc_final: 0.8293 (tp) REVERT: A 830 PHE cc_start: 0.6555 (OUTLIER) cc_final: 0.6299 (m-10) REVERT: A 950 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7992 (tt) REVERT: A 1435 LYS cc_start: 0.8028 (ptpp) cc_final: 0.7452 (ptpt) outliers start: 20 outliers final: 14 residues processed: 122 average time/residue: 1.1459 time to fit residues: 152.3124 Evaluate side-chains 118 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 675 THR Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 680 SER 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 92 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 98 optimal weight: 0.4980 chunk 76 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 chunk 11 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 60 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 696 ASN A 980 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 = 0.3945 r_free = 0.3945 target = 0.168132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.145469 restraints weight = 11152.196| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 1.63 r_work: 0.3649 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3529 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2349 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= 0.136 Angle : 0.589 9.013 14576 Z= 0.297 Chirality : 0.044 0.421 1629 Planarity : 0.004 0.051 1676 Dihedral : 17.003 174.938 2029 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.38 % Allowed : 20.09 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.24), residues: 1154 helix: 0.78 (0.30), residues: 316 sheet: -0.81 (0.35), residues: 181 loop : -1.08 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 612 HIS 0.004 0.001 HIS A 727 PHE 0.013 0.001 PHE A1520 TYR 0.014 0.001 TYR A 925 ARG 0.005 0.000 ARG A 467 Details of bonding type rmsd hydrogen bonds : bond 0.03764 ( 346) hydrogen bonds : angle 4.85159 ( 1027) metal coordination : bond 0.00855 ( 16) metal coordination : angle 4.47631 ( 21) covalent geometry : bond 0.00309 (10593) covalent geometry : angle 0.56485 (14555) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8110.12 seconds wall clock time: 142 minutes 27.72 seconds (8547.72 seconds total)