Starting phenix.real_space_refine on Sat Jul 26 08:44:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jk4_61543/07_2025/9jk4_61543.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jk4_61543/07_2025/9jk4_61543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jk4_61543/07_2025/9jk4_61543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jk4_61543/07_2025/9jk4_61543.map" model { file = "/net/cci-nas-00/data/ceres_data/9jk4_61543/07_2025/9jk4_61543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jk4_61543/07_2025/9jk4_61543.cif" } resolution = 2.82 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= -0.002 sd= 0.085 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 63 5.16 5 C 5382 2.51 5 N 1421 2.21 5 O 1491 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 8358 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8250 Classifications: {'peptide': 1048} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 54, 'TRANS': 993} Chain breaks: 8 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.34, per 1000 atoms: 0.64 Number of scatterers: 8358 At special positions: 0 Unit cell: (81.2446, 86.7341, 162.489, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 P 1 15.00 O 1491 8.00 N 1421 7.00 C 5382 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG B 1 " - " ASN A1202 " " NAG C 1 " - " ASN A1205 " Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 1.0 seconds 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1990 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 6 sheets defined 57.3% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 18 through 44 Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 66 through 82 Processing helix chain 'A' and resid 93 through 122 removed outlier: 3.515A pdb=" N VAL A 97 " --> pdb=" O GLY A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 141 Processing helix chain 'A' and resid 148 through 152 removed outlier: 3.752A pdb=" N TYR A 152 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 249 through 260 removed outlier: 4.288A pdb=" N ASN A 253 " --> pdb=" O PRO A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 302 Proline residue: A 286 - end of helix Processing helix chain 'A' and resid 309 through 323 Processing helix chain 'A' and resid 324 through 326 No H-bonds generated for 'chain 'A' and resid 324 through 326' Processing helix chain 'A' and resid 329 through 350 Processing helix chain 'A' and resid 375 through 392 Processing helix chain 'A' and resid 402 through 408 Processing helix chain 'A' and resid 578 through 594 Proline residue: A 584 - end of helix Processing helix chain 'A' and resid 595 through 616 removed outlier: 3.528A pdb=" N GLU A 600 " --> pdb=" O ALA A 596 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 638 removed outlier: 3.511A pdb=" N ALA A 634 " --> pdb=" O LEU A 630 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY A 638 " --> pdb=" O ALA A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 645 removed outlier: 3.570A pdb=" N LYS A 644 " --> pdb=" O PRO A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 712 Processing helix chain 'A' and resid 726 through 744 removed outlier: 3.550A pdb=" N LEU A 742 " --> pdb=" O GLN A 738 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER A 743 " --> pdb=" O ARG A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 763 Processing helix chain 'A' and resid 814 through 819 Processing helix chain 'A' and resid 834 through 847 removed outlier: 3.545A pdb=" N ASN A 846 " --> pdb=" O ASP A 842 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA A 847 " --> pdb=" O GLY A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 869 removed outlier: 4.051A pdb=" N VAL A 864 " --> pdb=" O LEU A 860 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE A 865 " --> pdb=" O LYS A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 965 removed outlier: 3.574A pdb=" N VAL A 958 " --> pdb=" O GLY A 954 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ARG A 959 " --> pdb=" O ILE A 955 " (cutoff:3.500A) Proline residue: A 960 - end of helix Processing helix chain 'A' and resid 979 through 993 removed outlier: 3.516A pdb=" N TYR A 993 " --> pdb=" O ILE A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1015 removed outlier: 4.519A pdb=" N LEU A1011 " --> pdb=" O ARG A1007 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A1014 " --> pdb=" O CYS A1010 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER A1015 " --> pdb=" O LEU A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1060 removed outlier: 3.528A pdb=" N LEU A1054 " --> pdb=" O SER A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1073 No H-bonds generated for 'chain 'A' and resid 1071 through 1073' Processing helix chain 'A' and resid 1074 through 1114 removed outlier: 3.533A pdb=" N LEU A1103 " --> pdb=" O CYS A1099 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1130 Processing helix chain 'A' and resid 1130 through 1138 Processing helix chain 'A' and resid 1139 through 1141 No H-bonds generated for 'chain 'A' and resid 1139 through 1141' Processing helix chain 'A' and resid 1147 through 1151 removed outlier: 3.847A pdb=" N MET A1151 " --> pdb=" O ILE A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1161 through 1201 removed outlier: 5.171A pdb=" N LEU A1178 " --> pdb=" O LEU A1174 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N THR A1179 " --> pdb=" O LYS A1175 " (cutoff:3.500A) Processing helix chain 'A' and resid 1225 through 1252 removed outlier: 4.080A pdb=" N THR A1250 " --> pdb=" O PHE A1246 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS A1251 " --> pdb=" O ILE A1247 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1265 Processing helix chain 'A' and resid 1266 through 1291 Proline residue: A1274 - end of helix Processing helix chain 'A' and resid 1306 through 1348 removed outlier: 3.626A pdb=" N TRP A1310 " --> pdb=" O PRO A1306 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A1317 " --> pdb=" O GLY A1313 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A1318 " --> pdb=" O CYS A1314 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 173 through 178 removed outlier: 4.231A pdb=" N TRP A 167 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 200 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 879 through 880 removed outlier: 6.344A pdb=" N ILE A 879 " --> pdb=" O THR A 976 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N PHE A 975 " --> pdb=" O PHE A 851 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR A 853 " --> pdb=" O PHE A 975 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL A 412 " --> pdb=" O CYS A 998 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LEU A1000 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N CYS A 414 " --> pdb=" O LEU A1000 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N SER A1002 " --> pdb=" O CYS A 414 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR A 997 " --> pdb=" O ILE A1017 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N ILE A1019 " --> pdb=" O THR A 997 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N CYS A 999 " --> pdb=" O ILE A1019 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N LEU A1021 " --> pdb=" O CYS A 999 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLY A1001 " --> pdb=" O LEU A1021 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 552 through 557 removed outlier: 3.924A pdb=" N GLU A 554 " --> pdb=" O PHE A 434 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N PHE A 434 " --> pdb=" O GLU A 554 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A 556 " --> pdb=" O VAL A 432 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N GLN A 830 " --> pdb=" O PRO A 429 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR A 431 " --> pdb=" O SER A 828 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLY A 825 " --> pdb=" O PHE A 749 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE A 749 " --> pdb=" O GLY A 825 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N GLN A 821 " --> pdb=" O CYS A 713 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP A 715 " --> pdb=" O GLN A 821 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 552 through 557 removed outlier: 3.924A pdb=" N GLU A 554 " --> pdb=" O PHE A 434 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N PHE A 434 " --> pdb=" O GLU A 554 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A 556 " --> pdb=" O VAL A 432 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N GLN A 830 " --> pdb=" O PRO A 429 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR A 431 " --> pdb=" O SER A 828 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLY A 825 " --> pdb=" O PHE A 749 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE A 749 " --> pdb=" O GLY A 825 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER A 702 " --> pdb=" O ALA A 750 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS A 752 " --> pdb=" O MET A 700 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N SER A 683 " --> pdb=" O ARG A 657 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LYS A 691 " --> pdb=" O GLN A 649 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLN A 649 " --> pdb=" O LYS A 691 " (cutoff:3.500A) removed outlier: 9.035A pdb=" N ILE A 767 " --> pdb=" O HIS A 652 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ALA A 654 " --> pdb=" O ILE A 767 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LEU A 769 " --> pdb=" O ALA A 654 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N TYR A 656 " --> pdb=" O LEU A 769 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 559 through 560 Processing sheet with id=AA6, first strand: chain 'A' and resid 756 through 757 480 hydrogen bonds defined for protein. 1389 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.39 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1496 1.33 - 1.45: 2092 1.45 - 1.57: 4869 1.57 - 1.70: 2 1.70 - 1.82: 85 Bond restraints: 8544 Sorted by residual: bond pdb=" C1 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.08e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.97e+00 bond pdb=" C5 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.16e+00 bond pdb=" C5 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.09e+00 bond pdb=" C3 NAG B 1 " pdb=" O3 NAG B 1 " ideal model delta sigma weight residual 1.403 1.424 -0.021 2.00e-02 2.50e+03 1.08e+00 ... (remaining 8539 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 11482 2.36 - 4.73: 107 4.73 - 7.09: 10 7.09 - 9.46: 1 9.46 - 11.82: 1 Bond angle restraints: 11601 Sorted by residual: angle pdb=" CB MET A 555 " pdb=" CG MET A 555 " pdb=" SD MET A 555 " ideal model delta sigma weight residual 112.70 124.52 -11.82 3.00e+00 1.11e-01 1.55e+01 angle pdb=" N GLN A1289 " pdb=" CA GLN A1289 " pdb=" C GLN A1289 " ideal model delta sigma weight residual 113.88 109.33 4.55 1.23e+00 6.61e-01 1.37e+01 angle pdb=" C LEU A1288 " pdb=" CA LEU A1288 " pdb=" CB LEU A1288 " ideal model delta sigma weight residual 110.27 104.71 5.56 1.94e+00 2.66e-01 8.20e+00 angle pdb=" CB MET A 826 " pdb=" CG MET A 826 " pdb=" SD MET A 826 " ideal model delta sigma weight residual 112.70 120.89 -8.19 3.00e+00 1.11e-01 7.46e+00 angle pdb=" CG MET A 826 " pdb=" SD MET A 826 " pdb=" CE MET A 826 " ideal model delta sigma weight residual 100.90 106.48 -5.58 2.20e+00 2.07e-01 6.43e+00 ... (remaining 11596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.15: 4582 21.15 - 42.30: 476 42.30 - 63.45: 107 63.45 - 84.60: 12 84.60 - 105.75: 12 Dihedral angle restraints: 5189 sinusoidal: 2142 harmonic: 3047 Sorted by residual: dihedral pdb=" C2 NAG B 2 " pdb=" C3 NAG B 2 " pdb=" C4 NAG B 2 " pdb=" O4 NAG B 2 " ideal model delta sinusoidal sigma weight residual 175.11 69.36 105.75 1 3.00e+01 1.11e-03 1.36e+01 dihedral pdb=" C2 NAG B 2 " pdb=" C3 NAG B 2 " pdb=" C4 NAG B 2 " pdb=" C5 NAG B 2 " ideal model delta sinusoidal sigma weight residual 53.78 -51.56 105.34 1 3.00e+01 1.11e-03 1.35e+01 dihedral pdb=" O3 NAG B 2 " pdb=" C3 NAG B 2 " pdb=" C4 NAG B 2 " pdb=" O4 NAG B 2 " ideal model delta sinusoidal sigma weight residual -64.55 -169.21 104.66 1 3.00e+01 1.11e-03 1.34e+01 ... (remaining 5186 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 953 0.034 - 0.069: 312 0.069 - 0.103: 73 0.103 - 0.138: 27 0.138 - 0.172: 3 Chirality restraints: 1368 Sorted by residual: chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A1202 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-01 2.50e+01 7.40e-01 chirality pdb=" CA ASN A 876 " pdb=" N ASN A 876 " pdb=" C ASN A 876 " pdb=" CB ASN A 876 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.24e-01 chirality pdb=" C4 NAG B 1 " pdb=" C3 NAG B 1 " pdb=" C5 NAG B 1 " pdb=" O4 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.39 -0.14 2.00e-01 2.50e+01 4.91e-01 ... (remaining 1365 not shown) Planarity restraints: 1442 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 313 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.32e+00 pdb=" C THR A 313 " -0.050 2.00e-02 2.50e+03 pdb=" O THR A 313 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU A 314 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 281 " 0.011 2.00e-02 2.50e+03 2.32e-02 5.37e+00 pdb=" C LEU A 281 " -0.040 2.00e-02 2.50e+03 pdb=" O LEU A 281 " 0.015 2.00e-02 2.50e+03 pdb=" N HIS A 282 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 157 " 0.029 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO A 158 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 158 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 158 " 0.025 5.00e-02 4.00e+02 ... (remaining 1439 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1820 2.78 - 3.31: 7595 3.31 - 3.84: 13650 3.84 - 4.37: 15961 4.37 - 4.90: 28257 Nonbonded interactions: 67283 Sorted by model distance: nonbonded pdb=" O SER A1050 " pdb=" OG SER A1050 " model vdw 2.252 3.040 nonbonded pdb=" O GLN A1289 " pdb=" NH2 ARG A1294 " model vdw 2.273 3.120 nonbonded pdb=" O TRP A 875 " pdb=" ND2 ASN A 876 " model vdw 2.284 3.120 nonbonded pdb=" O ASP A 595 " pdb=" OG1 THR A 599 " model vdw 2.284 3.040 nonbonded pdb=" O PHE A1012 " pdb=" OG SER A1018 " model vdw 2.291 3.040 ... (remaining 67278 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 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } 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: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.640 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:13.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 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 0.045 8548 Z= 0.144 Angle : 0.567 11.825 11613 Z= 0.277 Chirality : 0.038 0.172 1368 Planarity : 0.004 0.045 1440 Dihedral : 17.967 105.749 3199 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.13 % Allowed : 21.13 % Favored : 76.73 % 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: 0.87 (0.27), residues: 1030 helix: 1.38 (0.23), residues: 540 sheet: -1.09 (0.45), residues: 111 loop : 0.09 (0.34), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 875 HIS 0.003 0.001 HIS A 166 PHE 0.009 0.001 PHE A 292 TYR 0.013 0.001 TYR A 312 ARG 0.002 0.000 ARG A 601 Details of bonding type rmsd link_NAG-ASN : bond 0.00338 ( 2) link_NAG-ASN : angle 3.37453 ( 6) link_BETA1-4 : bond 0.00268 ( 2) link_BETA1-4 : angle 2.54058 ( 6) hydrogen bonds : bond 0.22726 ( 470) hydrogen bonds : angle 6.85083 ( 1389) covalent geometry : bond 0.00338 ( 8544) covalent geometry : angle 0.55917 (11601) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.873 Fit side-chains REVERT: A 754 MET cc_start: 0.0537 (mtp) cc_final: -0.1149 (tpp) REVERT: A 981 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.6951 (mp0) REVERT: A 1345 GLN cc_start: 0.7574 (mt0) cc_final: 0.6893 (mm-40) outliers start: 20 outliers final: 11 residues processed: 94 average time/residue: 1.1779 time to fit residues: 119.1457 Evaluate side-chains 86 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 981 GLU Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1122 THR Chi-restraints excluded: chain A residue 1193 SER Chi-restraints excluded: chain A residue 1224 ASP Chi-restraints excluded: chain A residue 1320 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 0.1980 chunk 60 optimal weight: 8.9990 chunk 94 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 HIS ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 376 GLN ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 GLN A 876 ASN A 956 HIS A 957 GLN A1014 GLN ** A1192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1214 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.180441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.102866 restraints weight = 9438.402| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.24 r_work: 0.3109 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8548 Z= 0.164 Angle : 0.619 11.071 11613 Z= 0.305 Chirality : 0.041 0.186 1368 Planarity : 0.005 0.043 1440 Dihedral : 9.602 87.694 1258 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.59 % Allowed : 17.93 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.38 (0.27), residues: 1030 helix: 2.01 (0.22), residues: 558 sheet: -1.13 (0.45), residues: 109 loop : -0.05 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 310 HIS 0.003 0.001 HIS A 166 PHE 0.028 0.002 PHE A 823 TYR 0.013 0.001 TYR A 312 ARG 0.003 0.000 ARG A 127 Details of bonding type rmsd link_NAG-ASN : bond 0.00516 ( 2) link_NAG-ASN : angle 2.55100 ( 6) link_BETA1-4 : bond 0.00299 ( 2) link_BETA1-4 : angle 2.24692 ( 6) hydrogen bonds : bond 0.06499 ( 470) hydrogen bonds : angle 4.67103 ( 1389) covalent geometry : bond 0.00388 ( 8544) covalent geometry : angle 0.61420 (11601) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 83 time to evaluate : 0.887 Fit side-chains REVERT: A 433 LEU cc_start: 0.6466 (OUTLIER) cc_final: 0.6069 (pp) REVERT: A 602 LEU cc_start: -0.0741 (OUTLIER) cc_final: -0.1307 (mt) REVERT: A 754 MET cc_start: 0.0763 (mtp) cc_final: -0.0694 (tpp) REVERT: A 872 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7518 (mp0) outliers start: 43 outliers final: 15 residues processed: 113 average time/residue: 1.1223 time to fit residues: 136.4289 Evaluate side-chains 89 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 1092 CYS Chi-restraints excluded: chain A residue 1122 THR Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1302 LEU Chi-restraints excluded: chain A residue 1320 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 2 optimal weight: 0.9990 chunk 42 optimal weight: 20.0000 chunk 27 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN A 282 HIS ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 ASN A 956 HIS A 957 GLN A1214 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.180604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.113777 restraints weight = 9429.970| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.32 r_work: 0.3049 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8548 Z= 0.152 Angle : 0.597 9.009 11613 Z= 0.289 Chirality : 0.040 0.161 1368 Planarity : 0.004 0.043 1440 Dihedral : 7.711 82.757 1246 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.80 % Allowed : 17.93 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.67 (0.27), residues: 1030 helix: 2.31 (0.22), residues: 558 sheet: -1.10 (0.45), residues: 109 loop : -0.03 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 310 HIS 0.003 0.001 HIS A1253 PHE 0.022 0.002 PHE A 823 TYR 0.013 0.001 TYR A 312 ARG 0.003 0.000 ARG A1254 Details of bonding type rmsd link_NAG-ASN : bond 0.00749 ( 2) link_NAG-ASN : angle 2.73470 ( 6) link_BETA1-4 : bond 0.00297 ( 2) link_BETA1-4 : angle 2.04144 ( 6) hydrogen bonds : bond 0.05785 ( 470) hydrogen bonds : angle 4.41220 ( 1389) covalent geometry : bond 0.00360 ( 8544) covalent geometry : angle 0.59187 (11601) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 79 time to evaluate : 0.922 Fit side-chains REVERT: A 48 LYS cc_start: 0.7923 (tptt) cc_final: 0.7641 (tptt) REVERT: A 122 ARG cc_start: 0.8160 (mtm180) cc_final: 0.7853 (mmm-85) REVERT: A 433 LEU cc_start: 0.6688 (OUTLIER) cc_final: 0.6159 (pp) REVERT: A 602 LEU cc_start: -0.0673 (OUTLIER) cc_final: -0.1263 (mt) REVERT: A 754 MET cc_start: 0.0828 (mtp) cc_final: -0.0426 (tpp) REVERT: A 872 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7644 (mp0) REVERT: A 959 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7417 (ttm170) REVERT: A 1070 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7940 (pm20) REVERT: A 1340 LYS cc_start: 0.8548 (mttm) cc_final: 0.7882 (tmmm) outliers start: 45 outliers final: 18 residues processed: 111 average time/residue: 1.0449 time to fit residues: 124.8845 Evaluate side-chains 98 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 879 ILE Chi-restraints excluded: chain A residue 959 ARG Chi-restraints excluded: chain A residue 1070 GLU Chi-restraints excluded: chain A residue 1092 CYS Chi-restraints excluded: chain A residue 1122 THR Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1302 LEU Chi-restraints excluded: chain A residue 1341 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 85 optimal weight: 0.0010 chunk 41 optimal weight: 0.5980 chunk 69 optimal weight: 0.0570 chunk 13 optimal weight: 0.0000 chunk 101 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 chunk 92 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.2708 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 HIS ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 ASN A 956 HIS A1214 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.183689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.107322 restraints weight = 9430.015| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.15 r_work: 0.3156 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8548 Z= 0.109 Angle : 0.544 9.577 11613 Z= 0.265 Chirality : 0.038 0.167 1368 Planarity : 0.004 0.043 1440 Dihedral : 6.724 76.940 1241 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.95 % Allowed : 19.10 % Favored : 76.95 % 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: 1.84 (0.27), residues: 1030 helix: 2.47 (0.22), residues: 557 sheet: -1.10 (0.45), residues: 109 loop : 0.05 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 310 HIS 0.003 0.000 HIS A 878 PHE 0.018 0.001 PHE A 823 TYR 0.011 0.001 TYR A 312 ARG 0.003 0.000 ARG A1068 Details of bonding type rmsd link_NAG-ASN : bond 0.00208 ( 2) link_NAG-ASN : angle 2.20893 ( 6) link_BETA1-4 : bond 0.00465 ( 2) link_BETA1-4 : angle 2.22691 ( 6) hydrogen bonds : bond 0.04680 ( 470) hydrogen bonds : angle 4.19637 ( 1389) covalent geometry : bond 0.00229 ( 8544) covalent geometry : angle 0.53988 (11601) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 83 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: A 48 LYS cc_start: 0.7869 (tptt) cc_final: 0.7564 (mmpt) REVERT: A 118 ARG cc_start: 0.7202 (ttm170) cc_final: 0.6549 (ttm-80) REVERT: A 122 ARG cc_start: 0.7948 (mtm180) cc_final: 0.7666 (mtt180) REVERT: A 140 ARG cc_start: 0.7448 (ttp-110) cc_final: 0.6646 (tpm170) REVERT: A 433 LEU cc_start: 0.6634 (OUTLIER) cc_final: 0.6143 (pp) REVERT: A 555 MET cc_start: 0.3905 (mmp) cc_final: 0.3474 (mmm) REVERT: A 602 LEU cc_start: -0.0652 (OUTLIER) cc_final: -0.1228 (mt) REVERT: A 700 MET cc_start: 0.1564 (ptp) cc_final: -0.0366 (ttt) REVERT: A 824 MET cc_start: 0.0527 (OUTLIER) cc_final: -0.1343 (pp-130) REVERT: A 872 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7569 (mp0) REVERT: A 1248 SER cc_start: 0.8771 (m) cc_final: 0.8518 (p) REVERT: A 1311 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7723 (mp) REVERT: A 1340 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7650 (tmmm) outliers start: 37 outliers final: 13 residues processed: 107 average time/residue: 1.4227 time to fit residues: 161.1712 Evaluate side-chains 93 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 842 ASP Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 876 ASN Chi-restraints excluded: chain A residue 1053 GLN Chi-restraints excluded: chain A residue 1092 CYS Chi-restraints excluded: chain A residue 1122 THR Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1302 LEU Chi-restraints excluded: chain A residue 1311 LEU Chi-restraints excluded: chain A residue 1340 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 56 optimal weight: 20.0000 chunk 89 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 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 282 HIS ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 ASN A 956 HIS A1214 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.182598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.107218 restraints weight = 9366.007| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.19 r_work: 0.3091 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8548 Z= 0.146 Angle : 0.567 9.399 11613 Z= 0.276 Chirality : 0.039 0.170 1368 Planarity : 0.004 0.043 1440 Dihedral : 6.681 75.198 1240 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.38 % Allowed : 19.21 % Favored : 76.41 % 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: 1.85 (0.27), residues: 1030 helix: 2.48 (0.22), residues: 560 sheet: -1.09 (0.44), residues: 109 loop : 0.03 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 310 HIS 0.004 0.001 HIS A1253 PHE 0.022 0.001 PHE A 823 TYR 0.012 0.001 TYR A 312 ARG 0.002 0.000 ARG A1068 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 2) link_NAG-ASN : angle 2.29595 ( 6) link_BETA1-4 : bond 0.00266 ( 2) link_BETA1-4 : angle 2.27990 ( 6) hydrogen bonds : bond 0.05158 ( 470) hydrogen bonds : angle 4.17467 ( 1389) covalent geometry : bond 0.00350 ( 8544) covalent geometry : angle 0.56262 (11601) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 72 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.7830 (tptt) cc_final: 0.7542 (mmpt) REVERT: A 118 ARG cc_start: 0.7196 (ttm170) cc_final: 0.6547 (ttm-80) REVERT: A 122 ARG cc_start: 0.7917 (mtm180) cc_final: 0.7632 (mtt180) REVERT: A 433 LEU cc_start: 0.6704 (OUTLIER) cc_final: 0.6190 (pp) REVERT: A 555 MET cc_start: 0.3895 (mmp) cc_final: 0.3499 (mmm) REVERT: A 602 LEU cc_start: -0.0545 (OUTLIER) cc_final: -0.1126 (mt) REVERT: A 754 MET cc_start: 0.0751 (mmm) cc_final: -0.0872 (tpp) REVERT: A 872 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7504 (mp0) REVERT: A 959 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7334 (ttm170) REVERT: A 1070 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7852 (pm20) REVERT: A 1311 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7711 (mp) REVERT: A 1340 LYS cc_start: 0.8371 (mttm) cc_final: 0.7663 (tmmm) outliers start: 41 outliers final: 20 residues processed: 103 average time/residue: 2.9540 time to fit residues: 315.8342 Evaluate side-chains 93 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 67 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 876 ASN Chi-restraints excluded: chain A residue 959 ARG Chi-restraints excluded: chain A residue 1053 GLN Chi-restraints excluded: chain A residue 1070 GLU Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1092 CYS Chi-restraints excluded: chain A residue 1110 SER Chi-restraints excluded: chain A residue 1122 THR Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1302 LEU Chi-restraints excluded: chain A residue 1311 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 25 optimal weight: 0.0040 chunk 62 optimal weight: 4.9990 chunk 48 optimal weight: 50.0000 chunk 18 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 HIS ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 ASN A 956 HIS A1214 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.180393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.103929 restraints weight = 9393.888| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.14 r_work: 0.3115 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8548 Z= 0.155 Angle : 0.569 9.392 11613 Z= 0.277 Chirality : 0.040 0.172 1368 Planarity : 0.004 0.043 1440 Dihedral : 6.718 74.719 1240 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.74 % Allowed : 20.17 % Favored : 76.09 % 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: 1.87 (0.27), residues: 1030 helix: 2.48 (0.22), residues: 561 sheet: -1.03 (0.44), residues: 114 loop : 0.07 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 310 HIS 0.003 0.001 HIS A1253 PHE 0.019 0.001 PHE A 823 TYR 0.013 0.001 TYR A 312 ARG 0.002 0.000 ARG A1068 Details of bonding type rmsd link_NAG-ASN : bond 0.00317 ( 2) link_NAG-ASN : angle 2.25153 ( 6) link_BETA1-4 : bond 0.00228 ( 2) link_BETA1-4 : angle 2.26454 ( 6) hydrogen bonds : bond 0.05260 ( 470) hydrogen bonds : angle 4.16860 ( 1389) covalent geometry : bond 0.00378 ( 8544) covalent geometry : angle 0.56452 (11601) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 69 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.7806 (tptt) cc_final: 0.7571 (mmpt) REVERT: A 118 ARG cc_start: 0.7234 (ttm170) cc_final: 0.6521 (ttm-80) REVERT: A 122 ARG cc_start: 0.7916 (mtm180) cc_final: 0.7562 (mmm-85) REVERT: A 433 LEU cc_start: 0.6722 (OUTLIER) cc_final: 0.6157 (pp) REVERT: A 555 MET cc_start: 0.3672 (mmp) cc_final: 0.3304 (mmm) REVERT: A 602 LEU cc_start: -0.0540 (OUTLIER) cc_final: -0.1127 (mt) REVERT: A 754 MET cc_start: 0.0744 (mmm) cc_final: -0.0961 (tpp) REVERT: A 830 GLN cc_start: 0.7457 (mm-40) cc_final: 0.7221 (mm110) REVERT: A 872 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7533 (mp0) REVERT: A 959 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7333 (ttm170) REVERT: A 1011 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8292 (tt) REVERT: A 1070 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7863 (pm20) REVERT: A 1311 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7743 (mp) REVERT: A 1340 LYS cc_start: 0.8361 (mttm) cc_final: 0.7660 (tmmm) outliers start: 35 outliers final: 20 residues processed: 94 average time/residue: 1.3191 time to fit residues: 133.6916 Evaluate side-chains 95 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 68 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 876 ASN Chi-restraints excluded: chain A residue 959 ARG Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1053 GLN Chi-restraints excluded: chain A residue 1070 GLU Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1092 CYS Chi-restraints excluded: chain A residue 1122 THR Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1302 LEU Chi-restraints excluded: chain A residue 1311 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 45 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 chunk 56 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 HIS ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 ASN A 956 HIS A1214 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.181534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.115932 restraints weight = 9422.529| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.32 r_work: 0.3046 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8548 Z= 0.165 Angle : 0.577 9.298 11613 Z= 0.279 Chirality : 0.040 0.172 1368 Planarity : 0.004 0.043 1440 Dihedral : 6.609 74.139 1240 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.70 % Allowed : 19.74 % Favored : 75.56 % 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: 1.83 (0.27), residues: 1030 helix: 2.44 (0.22), residues: 563 sheet: -1.00 (0.44), residues: 114 loop : 0.01 (0.35), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 310 HIS 0.003 0.001 HIS A 166 PHE 0.022 0.002 PHE A 823 TYR 0.014 0.001 TYR A 312 ARG 0.003 0.000 ARG A1068 Details of bonding type rmsd link_NAG-ASN : bond 0.00322 ( 2) link_NAG-ASN : angle 2.30353 ( 6) link_BETA1-4 : bond 0.00194 ( 2) link_BETA1-4 : angle 2.23583 ( 6) hydrogen bonds : bond 0.05373 ( 470) hydrogen bonds : angle 4.14831 ( 1389) covalent geometry : bond 0.00406 ( 8544) covalent geometry : angle 0.57310 (11601) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 68 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.7912 (tptt) cc_final: 0.7626 (mmpt) REVERT: A 118 ARG cc_start: 0.7489 (ttm170) cc_final: 0.6766 (ttm-80) REVERT: A 122 ARG cc_start: 0.8002 (mtm180) cc_final: 0.7661 (mmm-85) REVERT: A 136 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7694 (tt0) REVERT: A 433 LEU cc_start: 0.6673 (OUTLIER) cc_final: 0.6108 (pp) REVERT: A 555 MET cc_start: 0.3764 (mmp) cc_final: 0.3355 (mmm) REVERT: A 602 LEU cc_start: -0.0481 (OUTLIER) cc_final: -0.1068 (mt) REVERT: A 754 MET cc_start: 0.0801 (mmm) cc_final: -0.0930 (tpp) REVERT: A 830 GLN cc_start: 0.7531 (mm-40) cc_final: 0.7252 (mm110) REVERT: A 872 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7616 (mp0) REVERT: A 875 TRP cc_start: 0.7907 (t60) cc_final: 0.7604 (p-90) REVERT: A 876 ASN cc_start: 0.7053 (OUTLIER) cc_final: 0.6848 (p0) REVERT: A 959 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7423 (ttm170) REVERT: A 1011 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8372 (tt) REVERT: A 1070 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7881 (pm20) REVERT: A 1311 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7877 (mp) REVERT: A 1340 LYS cc_start: 0.8463 (mttm) cc_final: 0.7781 (tmmm) outliers start: 44 outliers final: 24 residues processed: 100 average time/residue: 1.0567 time to fit residues: 114.1630 Evaluate side-chains 98 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 65 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLN Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain A residue 578 HIS Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 781 MET Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 876 ASN Chi-restraints excluded: chain A residue 959 ARG Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1053 GLN Chi-restraints excluded: chain A residue 1070 GLU Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1092 CYS Chi-restraints excluded: chain A residue 1110 SER Chi-restraints excluded: chain A residue 1122 THR Chi-restraints excluded: chain A residue 1151 MET Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1302 LEU Chi-restraints excluded: chain A residue 1311 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 12 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 94 optimal weight: 0.8980 chunk 60 optimal weight: 9.9990 chunk 27 optimal weight: 0.4980 chunk 81 optimal weight: 0.3980 chunk 96 optimal weight: 0.0970 chunk 32 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 HIS ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 ASN A 956 HIS A1214 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.182183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.116090 restraints weight = 9399.273| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.30 r_work: 0.3104 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8548 Z= 0.116 Angle : 0.541 9.374 11613 Z= 0.263 Chirality : 0.038 0.172 1368 Planarity : 0.004 0.042 1440 Dihedral : 6.302 74.182 1240 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.16 % Allowed : 19.96 % Favored : 75.88 % 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: 1.97 (0.27), residues: 1030 helix: 2.58 (0.22), residues: 561 sheet: -0.95 (0.45), residues: 114 loop : 0.07 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 310 HIS 0.002 0.000 HIS A1253 PHE 0.018 0.001 PHE A 823 TYR 0.012 0.001 TYR A 312 ARG 0.002 0.000 ARG A1068 Details of bonding type rmsd link_NAG-ASN : bond 0.00191 ( 2) link_NAG-ASN : angle 2.23341 ( 6) link_BETA1-4 : bond 0.00258 ( 2) link_BETA1-4 : angle 2.21133 ( 6) hydrogen bonds : bond 0.04747 ( 470) hydrogen bonds : angle 4.06511 ( 1389) covalent geometry : bond 0.00259 ( 8544) covalent geometry : angle 0.53645 (11601) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 68 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.7755 (tp30) cc_final: 0.7515 (tp30) REVERT: A 48 LYS cc_start: 0.7929 (tptt) cc_final: 0.7685 (mmpt) REVERT: A 118 ARG cc_start: 0.7415 (ttm170) cc_final: 0.6803 (ttm-80) REVERT: A 122 ARG cc_start: 0.8078 (mtm180) cc_final: 0.7844 (mtt180) REVERT: A 140 ARG cc_start: 0.7487 (ttp-110) cc_final: 0.6734 (tpm170) REVERT: A 433 LEU cc_start: 0.6866 (OUTLIER) cc_final: 0.6269 (pp) REVERT: A 555 MET cc_start: 0.3771 (mmp) cc_final: 0.3340 (mmm) REVERT: A 602 LEU cc_start: -0.0452 (OUTLIER) cc_final: -0.1065 (mt) REVERT: A 754 MET cc_start: 0.0862 (mmm) cc_final: -0.0835 (tpp) REVERT: A 830 GLN cc_start: 0.7584 (mm-40) cc_final: 0.7286 (mm110) REVERT: A 872 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7651 (mp0) REVERT: A 875 TRP cc_start: 0.7852 (t60) cc_final: 0.7610 (p-90) REVERT: A 959 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.7432 (ttm170) REVERT: A 1011 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8365 (tt) REVERT: A 1070 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7904 (pm20) REVERT: A 1340 LYS cc_start: 0.8452 (mttm) cc_final: 0.7817 (tmmm) outliers start: 39 outliers final: 25 residues processed: 97 average time/residue: 1.0961 time to fit residues: 114.7209 Evaluate side-chains 97 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 66 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain A residue 578 HIS Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 842 ASP Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 959 ARG Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1053 GLN Chi-restraints excluded: chain A residue 1070 GLU Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1092 CYS Chi-restraints excluded: chain A residue 1110 SER Chi-restraints excluded: chain A residue 1122 THR Chi-restraints excluded: chain A residue 1151 MET Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1302 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 95 optimal weight: 0.0270 chunk 102 optimal weight: 0.5980 chunk 21 optimal weight: 0.0980 chunk 44 optimal weight: 20.0000 chunk 83 optimal weight: 0.7980 chunk 67 optimal weight: 0.0060 chunk 48 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 overall best weight: 0.3054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 HIS ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 956 HIS A1214 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.183214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.117639 restraints weight = 9466.057| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.31 r_work: 0.3134 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8548 Z= 0.107 Angle : 0.526 9.386 11613 Z= 0.256 Chirality : 0.038 0.173 1368 Planarity : 0.004 0.042 1440 Dihedral : 6.078 75.052 1240 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.42 % Allowed : 20.70 % Favored : 75.88 % 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: 2.07 (0.27), residues: 1030 helix: 2.70 (0.22), residues: 554 sheet: -0.91 (0.45), residues: 114 loop : 0.09 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 310 HIS 0.002 0.000 HIS A1253 PHE 0.017 0.001 PHE A 823 TYR 0.011 0.001 TYR A 312 ARG 0.002 0.000 ARG A1068 Details of bonding type rmsd link_NAG-ASN : bond 0.00123 ( 2) link_NAG-ASN : angle 2.16919 ( 6) link_BETA1-4 : bond 0.00301 ( 2) link_BETA1-4 : angle 2.17341 ( 6) hydrogen bonds : bond 0.04486 ( 470) hydrogen bonds : angle 3.99108 ( 1389) covalent geometry : bond 0.00232 ( 8544) covalent geometry : angle 0.52172 (11601) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 69 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.7689 (tp30) cc_final: 0.7437 (tp30) REVERT: A 48 LYS cc_start: 0.7837 (tptt) cc_final: 0.7610 (mmpt) REVERT: A 118 ARG cc_start: 0.7329 (ttm170) cc_final: 0.6708 (ttm-80) REVERT: A 122 ARG cc_start: 0.8011 (mtm180) cc_final: 0.7772 (mtt180) REVERT: A 140 ARG cc_start: 0.7430 (ttp-110) cc_final: 0.6711 (tpm170) REVERT: A 433 LEU cc_start: 0.6785 (OUTLIER) cc_final: 0.6209 (pp) REVERT: A 555 MET cc_start: 0.3707 (mmp) cc_final: 0.3201 (mmm) REVERT: A 602 LEU cc_start: -0.0653 (OUTLIER) cc_final: -0.1154 (mt) REVERT: A 700 MET cc_start: 0.0807 (ptt) cc_final: -0.0314 (ttt) REVERT: A 754 MET cc_start: 0.0927 (mmm) cc_final: -0.0536 (tpp) REVERT: A 830 GLN cc_start: 0.7555 (mm-40) cc_final: 0.7258 (mm110) REVERT: A 872 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7617 (mp0) REVERT: A 959 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7429 (ttm170) REVERT: A 1011 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8309 (tt) REVERT: A 1070 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7961 (pm20) REVERT: A 1340 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.7735 (tmmm) REVERT: A 1345 GLN cc_start: 0.8079 (tt0) cc_final: 0.7869 (tt0) outliers start: 32 outliers final: 20 residues processed: 93 average time/residue: 1.1291 time to fit residues: 113.0977 Evaluate side-chains 91 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 64 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain A residue 578 HIS Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 959 ARG Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1053 GLN Chi-restraints excluded: chain A residue 1070 GLU Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1092 CYS Chi-restraints excluded: chain A residue 1110 SER Chi-restraints excluded: chain A residue 1122 THR Chi-restraints excluded: chain A residue 1151 MET Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1302 LEU Chi-restraints excluded: chain A residue 1340 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 74 optimal weight: 0.2980 chunk 73 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 64 optimal weight: 0.4980 chunk 101 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 50 optimal weight: 40.0000 chunk 35 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 HIS ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 ASN A 956 HIS A1214 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.181966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.116351 restraints weight = 9345.539| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.31 r_work: 0.3082 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8548 Z= 0.122 Angle : 0.541 9.351 11613 Z= 0.264 Chirality : 0.038 0.174 1368 Planarity : 0.004 0.043 1440 Dihedral : 6.072 74.888 1240 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.09 % Allowed : 21.13 % Favored : 75.77 % 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: 2.12 (0.27), residues: 1030 helix: 2.73 (0.22), residues: 555 sheet: -0.85 (0.46), residues: 114 loop : 0.10 (0.35), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 47 HIS 0.003 0.001 HIS A1253 PHE 0.016 0.001 PHE A 823 TYR 0.012 0.001 TYR A 312 ARG 0.002 0.000 ARG A1068 Details of bonding type rmsd link_NAG-ASN : bond 0.00178 ( 2) link_NAG-ASN : angle 2.19646 ( 6) link_BETA1-4 : bond 0.00244 ( 2) link_BETA1-4 : angle 2.11500 ( 6) hydrogen bonds : bond 0.04704 ( 470) hydrogen bonds : angle 3.97909 ( 1389) covalent geometry : bond 0.00285 ( 8544) covalent geometry : angle 0.53637 (11601) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 68 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.7719 (tp30) cc_final: 0.7469 (tp30) REVERT: A 118 ARG cc_start: 0.7421 (ttm170) cc_final: 0.6804 (ttm-80) REVERT: A 122 ARG cc_start: 0.8074 (mtm180) cc_final: 0.7834 (mtt180) REVERT: A 140 ARG cc_start: 0.7446 (ttp-110) cc_final: 0.6707 (tpm170) REVERT: A 555 MET cc_start: 0.3955 (mmp) cc_final: 0.2507 (pmm) REVERT: A 602 LEU cc_start: -0.0647 (OUTLIER) cc_final: -0.1148 (mt) REVERT: A 700 MET cc_start: 0.0714 (ptt) cc_final: -0.0708 (ttt) REVERT: A 830 GLN cc_start: 0.7535 (mm-40) cc_final: 0.7189 (mm110) REVERT: A 872 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7635 (mp0) REVERT: A 959 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7446 (ttm170) REVERT: A 1011 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8378 (tt) REVERT: A 1070 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7914 (pm20) REVERT: A 1340 LYS cc_start: 0.8422 (mttm) cc_final: 0.7762 (tmmm) REVERT: A 1345 GLN cc_start: 0.8168 (tt0) cc_final: 0.7908 (tt0) outliers start: 29 outliers final: 19 residues processed: 89 average time/residue: 1.1983 time to fit residues: 114.7727 Evaluate side-chains 92 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 414 CYS Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain A residue 578 HIS Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 872 GLU Chi-restraints excluded: chain A residue 959 ARG Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1053 GLN Chi-restraints excluded: chain A residue 1070 GLU Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1092 CYS Chi-restraints excluded: chain A residue 1110 SER Chi-restraints excluded: chain A residue 1122 THR Chi-restraints excluded: chain A residue 1151 MET Chi-restraints excluded: chain A residue 1302 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 18 optimal weight: 0.0070 chunk 52 optimal weight: 7.9990 chunk 50 optimal weight: 40.0000 chunk 91 optimal weight: 0.0970 chunk 14 optimal weight: 0.3980 chunk 94 optimal weight: 0.5980 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 HIS ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 HIS ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 ASN A 956 HIS A1214 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.183530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.117781 restraints weight = 9495.920| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.25 r_work: 0.3129 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8548 Z= 0.106 Angle : 0.526 9.369 11613 Z= 0.257 Chirality : 0.038 0.175 1368 Planarity : 0.004 0.042 1440 Dihedral : 5.854 75.081 1240 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.99 % Allowed : 21.34 % Favored : 75.67 % 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: 2.17 (0.27), residues: 1030 helix: 2.77 (0.22), residues: 554 sheet: -0.80 (0.46), residues: 114 loop : 0.14 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 47 HIS 0.002 0.000 HIS A 878 PHE 0.016 0.001 PHE A 823 TYR 0.010 0.001 TYR A 312 ARG 0.002 0.000 ARG A1254 Details of bonding type rmsd link_NAG-ASN : bond 0.00136 ( 2) link_NAG-ASN : angle 2.16478 ( 6) link_BETA1-4 : bond 0.00313 ( 2) link_BETA1-4 : angle 2.06507 ( 6) hydrogen bonds : bond 0.04241 ( 470) hydrogen bonds : angle 3.90292 ( 1389) covalent geometry : bond 0.00236 ( 8544) covalent geometry : angle 0.52173 (11601) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7554.82 seconds wall clock time: 132 minutes 6.58 seconds (7926.58 seconds total)