Starting phenix.real_space_refine on Fri Feb 14 20:15:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gna_34158/02_2025/8gna_34158.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gna_34158/02_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_34158/02_2025/8gna_34158.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gna_34158/02_2025/8gna_34158.map" model { file = "/net/cci-nas-00/data/ceres_data/8gna_34158/02_2025/8gna_34158.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gna_34158/02_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 6.72, per 1000 atoms: 0.66 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: 2.61 Conformation dependent library (CDL) restraints added in 1.2 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: 4.41 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: 5.60 Time building geometry restraints manager: 3.02 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: 3.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 33.270 Find NCS groups from input model: 0.120 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:13.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.150 ------------------------------------------------------------------------------- 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 0.033 10593 Z= 0.168 Angle : 0.576 16.496 14555 Z= 0.319 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 *********************** 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 : 1.218 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 1.2655 time to fit residues: 213.5199 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 : 1.045 ------------------------------------------------------------------------------- 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 = 0.3907 r_free = 0.3907 target = 0.164338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.141660 restraints weight = 11060.083| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 1.62 r_work: 0.3619 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 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 10593 Z= 0.284 Angle : 0.625 7.956 14555 Z= 0.328 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 *********************** 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 : 1.112 Fit side-chains REVERT: A 351 LYS cc_start: 0.7782 (mmmm) cc_final: 0.7453 (mmtt) REVERT: A 415 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7630 (tt0) REVERT: A 498 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7447 (mp-120) REVERT: A 611 GLU cc_start: 0.8629 (pt0) cc_final: 0.8383 (pt0) REVERT: A 717 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7660 (mt-10) REVERT: A 1595 TYR cc_start: 0.8301 (t80) cc_final: 0.8083 (t80) outliers start: 19 outliers final: 6 residues processed: 130 average time/residue: 1.2491 time to fit residues: 176.2279 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 : 1.070 ------------------------------------------------------------------------------- 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: 0.6980 chunk 82 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 49 optimal weight: 0.1980 chunk 80 optimal weight: 0.0170 chunk 98 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- 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 = 0.3934 r_free = 0.3934 target = 0.167291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.144858 restraints weight = 11175.626| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 1.62 r_work: 0.3655 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3536 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10593 Z= 0.201 Angle : 0.559 7.878 14555 Z= 0.297 Chirality : 0.043 0.406 1629 Planarity : 0.004 0.048 1676 Dihedral : 17.355 175.129 2029 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.48 % Allowed : 13.50 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.24), residues: 1154 helix: 0.56 (0.30), residues: 313 sheet: -0.30 (0.40), residues: 148 loop : -1.07 (0.23), residues: 693 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 0.012 0.001 PHE A 284 TYR 0.011 0.001 TYR A1595 ARG 0.005 0.000 ARG A1505 *********************** 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 138 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 1.042 Fit side-chains REVERT: A 717 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7627 (mt-10) REVERT: A 830 PHE cc_start: 0.7042 (m-10) cc_final: 0.6786 (m-10) REVERT: A 1435 LYS cc_start: 0.8185 (ptpp) cc_final: 0.7350 (mttt) outliers start: 23 outliers final: 9 residues processed: 128 average time/residue: 1.2334 time to fit residues: 170.8639 Evaluate side-chains 108 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL 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 675 THR Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 880 ILE Chi-restraints excluded: chain A residue 1423 THR 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: 0.6980 chunk 6 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS A 287 ASN A 350 ASN A 434 GLN A 502 ASN ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 980 ASN ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.164464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.141837 restraints weight = 10992.821| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 1.61 r_work: 0.3615 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10593 Z= 0.265 Angle : 0.584 8.210 14555 Z= 0.307 Chirality : 0.045 0.422 1629 Planarity : 0.004 0.049 1676 Dihedral : 17.313 176.013 2029 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 3.67 % Allowed : 15.12 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.24), residues: 1154 helix: 0.52 (0.30), residues: 314 sheet: -0.61 (0.38), residues: 166 loop : -1.09 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 612 HIS 0.006 0.001 HIS A 455 PHE 0.015 0.001 PHE A1520 TYR 0.015 0.001 TYR A1595 ARG 0.004 0.000 ARG A 472 *********************** 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 149 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 115 time to evaluate : 1.096 Fit side-chains REVERT: A 498 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7299 (mp-120) REVERT: A 717 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7652 (mt-10) REVERT: A 830 PHE cc_start: 0.6993 (m-10) cc_final: 0.6754 (m-10) outliers start: 34 outliers final: 15 residues processed: 139 average time/residue: 1.2159 time to fit residues: 183.1192 Evaluate side-chains 117 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 1.185 ------------------------------------------------------------------------------- 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 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 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 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 34 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 114 optimal weight: 0.0770 chunk 71 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 980 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 = 0.3931 r_free = 0.3931 target = 0.166906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.144326 restraints weight = 11028.416| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 1.62 r_work: 0.3645 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10593 Z= 0.210 Angle : 0.559 8.077 14555 Z= 0.295 Chirality : 0.044 0.420 1629 Planarity : 0.004 0.048 1676 Dihedral : 17.252 175.196 2029 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 3.46 % Allowed : 16.41 % Favored : 80.13 % 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: 0.64 (0.30), residues: 314 sheet: -0.75 (0.37), residues: 167 loop : -1.06 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 612 HIS 0.004 0.001 HIS A 727 PHE 0.012 0.001 PHE A1520 TYR 0.016 0.001 TYR A1595 ARG 0.003 0.000 ARG A 719 *********************** 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 151 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 1.133 Fit side-chains REVERT: A 287 ASN cc_start: 0.7078 (m110) cc_final: 0.6757 (m110) REVERT: A 351 LYS cc_start: 0.7759 (mmmm) cc_final: 0.7429 (mmtt) REVERT: A 717 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7711 (mt-10) REVERT: A 783 LEU cc_start: 0.8652 (tp) cc_final: 0.8413 (tp) REVERT: A 830 PHE cc_start: 0.6798 (m-10) cc_final: 0.6532 (m-10) REVERT: A 1435 LYS cc_start: 0.8207 (ptpp) cc_final: 0.7653 (ptpt) outliers start: 32 outliers final: 17 residues processed: 141 average time/residue: 1.1059 time to fit residues: 170.1033 Evaluate side-chains 119 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 1.171 ------------------------------------------------------------------------------- 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 201 THR 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 66 optimal weight: 0.3980 chunk 63 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 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 93 GLN A 109 HIS A 434 GLN A 502 ASN A 696 ASN A 980 ASN ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.165855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.143261 restraints weight = 11160.405| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.63 r_work: 0.3622 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10593 Z= 0.231 Angle : 0.575 9.272 14555 Z= 0.300 Chirality : 0.044 0.421 1629 Planarity : 0.004 0.049 1676 Dihedral : 17.226 175.255 2029 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.78 % Allowed : 17.39 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.24), residues: 1154 helix: 0.64 (0.29), residues: 316 sheet: -0.75 (0.37), residues: 163 loop : -1.09 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 612 HIS 0.004 0.001 HIS A 455 PHE 0.014 0.001 PHE A1520 TYR 0.016 0.001 TYR A1595 ARG 0.004 0.000 ARG A 719 *********************** 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: 35 poor density : 110 time to evaluate : 1.193 Fit side-chains REVERT: A 287 ASN cc_start: 0.7084 (m110) cc_final: 0.6738 (m110) REVERT: A 351 LYS cc_start: 0.7776 (mmmm) cc_final: 0.7440 (mmtt) REVERT: A 498 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7358 (mp-120) REVERT: A 925 TYR cc_start: 0.7950 (m-80) cc_final: 0.7733 (m-80) REVERT: A 1435 LYS cc_start: 0.8190 (ptpp) cc_final: 0.7637 (ptpt) REVERT: A 1581 ARG cc_start: 0.7699 (tmt90) cc_final: 0.7364 (ttt90) outliers start: 35 outliers final: 19 residues processed: 134 average time/residue: 1.1999 time to fit residues: 174.9236 Evaluate side-chains 123 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 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 684 THR Chi-restraints excluded: chain A residue 778 ASN Chi-restraints excluded: chain A residue 880 ILE Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 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: 0.7980 chunk 98 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 93 optimal weight: 0.5980 chunk 118 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 287 ASN A 502 ASN A 696 ASN A 980 ASN ** A1418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.162249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.139363 restraints weight = 11293.616| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 1.64 r_work: 0.3594 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 10593 Z= 0.308 Angle : 0.608 8.214 14555 Z= 0.317 Chirality : 0.046 0.418 1629 Planarity : 0.005 0.053 1676 Dihedral : 17.280 175.484 2029 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 4.10 % Allowed : 17.39 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.99 (0.24), residues: 1154 helix: 0.43 (0.29), residues: 321 sheet: -0.94 (0.35), residues: 191 loop : -1.12 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 612 HIS 0.006 0.001 HIS A 455 PHE 0.016 0.002 PHE A1520 TYR 0.021 0.002 TYR A1595 ARG 0.007 0.001 ARG A 168 *********************** 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 142 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 104 time to evaluate : 1.096 Fit side-chains REVERT: A 31 LYS cc_start: 0.8569 (mppt) cc_final: 0.8333 (mptt) REVERT: A 194 THR cc_start: 0.8174 (OUTLIER) cc_final: 0.7960 (p) REVERT: A 498 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7209 (mp-120) REVERT: A 567 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7855 (tttp) REVERT: A 830 PHE cc_start: 0.6968 (OUTLIER) cc_final: 0.6710 (m-10) REVERT: A 925 TYR cc_start: 0.8044 (m-80) cc_final: 0.7805 (m-80) outliers start: 38 outliers final: 18 residues processed: 131 average time/residue: 1.0795 time to fit residues: 154.7790 Evaluate side-chains 113 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 1.147 ------------------------------------------------------------------------------- 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 194 THR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 567 LYS 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 778 ASN Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 880 ILE Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 1507 VAL Chi-restraints excluded: chain A residue 1509 THR Chi-restraints excluded: chain A residue 1585 SER Chi-restraints excluded: chain A residue 1639 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 68 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 78 optimal weight: 0.4980 chunk 41 optimal weight: 0.0970 chunk 109 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.3919 r_free = 0.3919 target = 0.165422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.142829 restraints weight = 11163.595| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 1.63 r_work: 0.3629 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10593 Z= 0.227 Angle : 0.575 8.133 14555 Z= 0.302 Chirality : 0.044 0.418 1629 Planarity : 0.004 0.051 1676 Dihedral : 17.239 174.704 2029 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.02 % Allowed : 19.33 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.97 (0.24), residues: 1154 helix: 0.49 (0.29), residues: 322 sheet: -0.90 (0.35), residues: 177 loop : -1.15 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 612 HIS 0.004 0.001 HIS A 727 PHE 0.013 0.001 PHE A1520 TYR 0.016 0.001 TYR A1595 ARG 0.005 0.000 ARG A 168 *********************** 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 131 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 1.124 Fit side-chains REVERT: A 31 LYS cc_start: 0.8540 (mppt) cc_final: 0.8300 (mptt) REVERT: A 194 THR cc_start: 0.8166 (OUTLIER) cc_final: 0.7965 (p) REVERT: A 498 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7154 (mp-120) REVERT: A 925 TYR cc_start: 0.7966 (m-80) cc_final: 0.7745 (m-80) REVERT: A 1581 ARG cc_start: 0.7709 (tmt90) cc_final: 0.7358 (tpt-90) outliers start: 28 outliers final: 15 residues processed: 125 average time/residue: 1.0859 time to fit residues: 148.4766 Evaluate side-chains 109 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 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 684 THR Chi-restraints excluded: chain A residue 778 ASN Chi-restraints excluded: chain A residue 880 ILE Chi-restraints excluded: chain A residue 950 LEU Chi-restraints excluded: chain A residue 1507 VAL Chi-restraints excluded: chain A residue 1509 THR 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: 0.6980 chunk 30 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 98 optimal weight: 0.4980 chunk 16 optimal weight: 0.1980 chunk 106 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 78 optimal weight: 0.0370 chunk 88 optimal weight: 0.4980 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** A 455 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3959 r_free = 0.3959 target = 0.169397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.146895 restraints weight = 11180.171| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 1.63 r_work: 0.3668 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3549 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10593 Z= 0.178 Angle : 0.553 8.198 14555 Z= 0.290 Chirality : 0.043 0.422 1629 Planarity : 0.004 0.050 1676 Dihedral : 17.122 174.370 2029 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.70 % Allowed : 19.44 % Favored : 77.86 % 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: -0.84 (0.24), residues: 1154 helix: 0.72 (0.29), residues: 317 sheet: -1.01 (0.34), residues: 185 loop : -1.06 (0.24), residues: 652 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 0.010 0.001 PHE A1520 TYR 0.013 0.001 TYR A1595 ARG 0.004 0.000 ARG A 168 *********************** 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 137 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 1.129 Fit side-chains REVERT: A 31 LYS cc_start: 0.8488 (mppt) cc_final: 0.8254 (mptt) REVERT: A 357 LYS cc_start: 0.7728 (mptp) cc_final: 0.7341 (ttmm) REVERT: A 830 PHE cc_start: 0.6491 (m-10) cc_final: 0.6265 (m-10) REVERT: A 1581 ARG cc_start: 0.7538 (tmt90) cc_final: 0.7335 (tpt-90) outliers start: 25 outliers final: 11 residues processed: 132 average time/residue: 1.0981 time to fit residues: 158.2207 Evaluate side-chains 109 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 1.041 ------------------------------------------------------------------------------- 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 237 ILE Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 413 THR 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 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 1 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 76 optimal weight: 0.0570 chunk 113 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 = 0.3934 r_free = 0.3934 target = 0.166907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.144381 restraints weight = 11165.731| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 1.61 r_work: 0.3634 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10593 Z= 0.218 Angle : 0.575 9.260 14555 Z= 0.299 Chirality : 0.044 0.421 1629 Planarity : 0.004 0.048 1676 Dihedral : 17.104 174.813 2029 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 1.84 % Allowed : 21.06 % Favored : 77.11 % 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: 0.75 (0.30), residues: 316 sheet: -0.95 (0.35), residues: 181 loop : -1.08 (0.24), residues: 657 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 0.013 0.001 PHE A1520 TYR 0.015 0.001 TYR A1595 ARG 0.007 0.000 ARG A 168 ********************** 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 119 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 1.145 Fit side-chains REVERT: A 31 LYS cc_start: 0.8506 (mppt) cc_final: 0.8271 (mptt) REVERT: A 351 LYS cc_start: 0.7791 (mmmm) cc_final: 0.7468 (mmtt) REVERT: A 357 LYS cc_start: 0.7702 (mptp) cc_final: 0.7321 (tppt) REVERT: A 783 LEU cc_start: 0.8682 (tp) cc_final: 0.8352 (tp) REVERT: A 830 PHE cc_start: 0.6528 (m-10) cc_final: 0.6284 (m-10) REVERT: A 1581 ARG cc_start: 0.7489 (tmt90) cc_final: 0.7281 (tpt-90) outliers start: 17 outliers final: 12 residues processed: 115 average time/residue: 1.1392 time to fit residues: 143.3829 Evaluate side-chains 112 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 237 ILE Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 413 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 92 optimal weight: 0.0870 chunk 118 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 32 optimal weight: 0.1980 chunk 11 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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 = 0.3950 r_free = 0.3950 target = 0.168557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.145878 restraints weight = 11118.292| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 1.64 r_work: 0.3658 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10593 Z= 0.193 Angle : 0.563 9.537 14555 Z= 0.294 Chirality : 0.043 0.421 1629 Planarity : 0.004 0.048 1676 Dihedral : 17.037 174.715 2029 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 1.73 % Allowed : 21.17 % Favored : 77.11 % 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: 0.80 (0.30), residues: 316 sheet: -0.94 (0.34), residues: 185 loop : -1.07 (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 0.012 0.001 PHE A 15 TYR 0.015 0.001 TYR A1595 ARG 0.005 0.000 ARG A 467 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6525.26 seconds wall clock time: 116 minutes 43.00 seconds (7003.00 seconds total)