Starting phenix.real_space_refine on Fri Jul 3 00:12:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ijl_35488/07_2026/8ijl_35488.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ijl_35488/07_2026/8ijl_35488.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ijl_35488/07_2026/8ijl_35488.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ijl_35488/07_2026/8ijl_35488.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ijl_35488/07_2026/8ijl_35488.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ijl_35488/07_2026/8ijl_35488.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ijl_35488/07_2026/8ijl_35488.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ijl_35488/07_2026/8ijl_35488.cif" } resolution = 2.62 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.034 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: 9 Type Number sf(0) Gaussians Al 1 5.89 5 P 7 5.49 5 Mg 1 5.21 5 S 47 5.16 5 Na 2 4.78 5 C 6731 2.51 5 N 1643 2.21 5 O 1924 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10360 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7638 Classifications: {'peptide': 982} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 35, 'TRANS': 946} Chain: "B" Number of atoms: 2165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2165 Classifications: {'peptide': 266} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 247} Chain breaks: 1 Chain: "A" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 429 Unusual residues: {' MG': 1, ' NA': 2, 'ADP': 1, 'ALF': 1, 'CLR': 1, 'PCW': 5, 'Q7G': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 120 Unusual residues: {'CLR': 1, 'NAG': 1, 'Q7G': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 41 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Time building chain proxies: 2.87, per 1000 atoms: 0.28 Number of scatterers: 10360 At special positions: 0 Unit cell: (75.53, 89.64, 175.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) S 47 16.00 P 7 15.00 Al 1 13.00 Mg 1 11.99 Na 2 11.00 F 4 9.00 O 1924 8.00 N 1643 7.00 C 6731 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 277 " distance=2.03 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=1, symmetry=0 Links applied NAG-ASN " NAG B 401 " - " ASN B 158 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 429.0 milliseconds 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2322 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 10 sheets defined 48.9% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 60 through 68 Processing helix chain 'A' and resid 77 through 89 removed outlier: 3.680A pdb=" N THR A 82 " --> pdb=" O SER A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 107 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 113 through 134 Processing helix chain 'A' and resid 140 through 163 Processing helix chain 'A' and resid 168 through 172 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 273 through 276 Processing helix chain 'A' and resid 277 through 289 Processing helix chain 'A' and resid 294 through 324 removed outlier: 3.663A pdb=" N ALA A 322 " --> pdb=" O PHE A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 344 Processing helix chain 'A' and resid 347 through 365 removed outlier: 3.626A pdb=" N LYS A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 379 removed outlier: 3.871A pdb=" N THR A 378 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 374 through 379' Processing helix chain 'A' and resid 429 through 440 Processing helix chain 'A' and resid 453 through 457 Processing helix chain 'A' and resid 462 through 477 Processing helix chain 'A' and resid 479 through 486 Processing helix chain 'A' and resid 522 through 529 Processing helix chain 'A' and resid 543 through 559 removed outlier: 3.558A pdb=" N SER A 549 " --> pdb=" O SER A 545 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS A 551 " --> pdb=" O ALA A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 621 Processing helix chain 'A' and resid 632 through 643 Processing helix chain 'A' and resid 652 through 661 removed outlier: 3.564A pdb=" N ALA A 657 " --> pdb=" O VAL A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 684 removed outlier: 3.650A pdb=" N ASP A 684 " --> pdb=" O MET A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 697 Processing helix chain 'A' and resid 706 through 719 Processing helix chain 'A' and resid 730 through 732 No H-bonds generated for 'chain 'A' and resid 730 through 732' Processing helix chain 'A' and resid 733 through 740 Processing helix chain 'A' and resid 751 through 757 Processing helix chain 'A' and resid 767 through 809 removed outlier: 4.269A pdb=" N VAL A 771 " --> pdb=" O PHE A 767 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS A 785 " --> pdb=" O PHE A 781 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS A 786 " --> pdb=" O ASP A 782 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS A 794 " --> pdb=" O TYR A 790 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASN A 795 " --> pdb=" O THR A 791 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE A 796 " --> pdb=" O LEU A 792 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA A 797 " --> pdb=" O THR A 793 " (cutoff:3.500A) Proline residue: A 801 - end of helix Processing helix chain 'A' and resid 815 through 825 removed outlier: 3.625A pdb=" N LEU A 820 " --> pdb=" O THR A 816 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 821 " --> pdb=" O ILE A 817 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 822 " --> pdb=" O THR A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 834 Processing helix chain 'A' and resid 835 through 837 No H-bonds generated for 'chain 'A' and resid 835 through 837' Processing helix chain 'A' and resid 842 through 846 removed outlier: 3.836A pdb=" N ARG A 846 " --> pdb=" O ILE A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 867 Processing helix chain 'A' and resid 868 through 887 removed outlier: 3.724A pdb=" N MET A 872 " --> pdb=" O HIS A 868 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 880 " --> pdb=" O GLY A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 896 removed outlier: 3.529A pdb=" N LEU A 895 " --> pdb=" O PRO A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 903 Processing helix chain 'A' and resid 919 through 949 removed outlier: 3.571A pdb=" N ALA A 944 " --> pdb=" O ILE A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 960 Processing helix chain 'A' and resid 964 through 984 removed outlier: 4.087A pdb=" N TRP A 968 " --> pdb=" O ASN A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1002 Processing helix chain 'A' and resid 1004 through 1025 Processing helix chain 'A' and resid 1028 through 1035 Processing helix chain 'B' and resid 30 through 60 removed outlier: 3.796A pdb=" N LYS B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N THR B 60 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 110 Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 114 through 118 removed outlier: 3.709A pdb=" N LYS B 118 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 156 Processing helix chain 'B' and resid 220 through 225 removed outlier: 3.977A pdb=" N LYS B 224 " --> pdb=" O GLU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 236 Processing helix chain 'B' and resid 242 through 244 No H-bonds generated for 'chain 'B' and resid 242 through 244' Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 193 removed outlier: 4.561A pdb=" N LEU A 182 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL A 202 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N CYS A 261 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL A 225 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLU A 263 " --> pdb=" O CYS A 223 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N CYS A 223 " --> pdb=" O GLU A 263 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE A 269 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N LEU A 217 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ILE A 271 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ILE A 215 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N CYS A 223 " --> pdb=" O ARG A 239 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 209 through 210 removed outlier: 6.570A pdb=" N CYS A 261 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL A 225 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLU A 263 " --> pdb=" O CYS A 223 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N CYS A 223 " --> pdb=" O GLU A 263 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE A 269 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N LEU A 217 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ILE A 271 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ILE A 215 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 368 through 370 removed outlier: 6.324A pdb=" N GLY A 743 " --> pdb=" O MET A 760 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LEU A 762 " --> pdb=" O GLY A 743 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ALA A 745 " --> pdb=" O LEU A 762 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL A 724 " --> pdb=" O ILE A 742 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ILE A 744 " --> pdb=" O VAL A 724 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL A 726 " --> pdb=" O ILE A 744 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N MET A 746 " --> pdb=" O VAL A 726 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N GLY A 728 " --> pdb=" O MET A 746 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N VAL A 625 " --> pdb=" O ILE A 700 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N PHE A 702 " --> pdb=" O VAL A 625 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N MET A 627 " --> pdb=" O PHE A 702 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 408 through 411 removed outlier: 5.236A pdb=" N VAL A 400 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ILE A 604 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 9.346A pdb=" N PHE A 595 " --> pdb=" O TYR A 571 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N TYR A 571 " --> pdb=" O PHE A 595 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N PHE A 597 " --> pdb=" O HIS A 569 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N HIS A 569 " --> pdb=" O PHE A 597 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY A 599 " --> pdb=" O PHE A 567 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE A 515 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N GLU A 506 " --> pdb=" O LYS A 488 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LYS A 488 " --> pdb=" O GLU A 506 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 408 through 411 removed outlier: 5.236A pdb=" N VAL A 400 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ILE A 604 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N CYS A 530 " --> pdb=" O PHE A 595 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N PHE A 597 " --> pdb=" O CYS A 530 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N THR A 532 " --> pdb=" O PHE A 597 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N GLY A 599 " --> pdb=" O THR A 532 " (cutoff:3.500A) removed outlier: 9.426A pdb=" N MET A 534 " --> pdb=" O GLY A 599 " (cutoff:3.500A) removed outlier: 12.537A pdb=" N LEU A 601 " --> pdb=" O MET A 534 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 444 through 445 removed outlier: 3.647A pdb=" N GLU A 444 " --> pdb=" O VAL A 460 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 910 through 911 Processing sheet with id=AA8, first strand: chain 'B' and resid 77 through 80 Processing sheet with id=AA9, first strand: chain 'B' and resid 87 through 90 Processing sheet with id=AB1, first strand: chain 'B' and resid 123 through 124 494 hydrogen bonds defined for protein. 1401 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: 1.83 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1644 1.32 - 1.44: 2663 1.44 - 1.57: 6174 1.57 - 1.69: 13 1.69 - 1.82: 78 Bond restraints: 10572 Sorted by residual: bond pdb=" C11 PCW A1105 " pdb=" O3 PCW A1105 " ideal model delta sigma weight residual 1.326 1.453 -0.127 2.00e-02 2.50e+03 4.05e+01 bond pdb=" C11 PCW A1104 " pdb=" O3 PCW A1104 " ideal model delta sigma weight residual 1.326 1.453 -0.127 2.00e-02 2.50e+03 4.01e+01 bond pdb=" C11 PCW A1108 " pdb=" O3 PCW A1108 " ideal model delta sigma weight residual 1.326 1.453 -0.127 2.00e-02 2.50e+03 4.00e+01 bond pdb=" C11 PCW A1107 " pdb=" O3 PCW A1107 " ideal model delta sigma weight residual 1.326 1.451 -0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" C31 PCW A1104 " pdb=" O2 PCW A1104 " ideal model delta sigma weight residual 1.333 1.455 -0.122 2.00e-02 2.50e+03 3.74e+01 ... (remaining 10567 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.08: 14328 14.08 - 28.17: 8 28.17 - 42.25: 0 42.25 - 56.33: 0 56.33 - 70.42: 2 Bond angle restraints: 14338 Sorted by residual: angle pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " pdb=" F2 ALF A1101 " ideal model delta sigma weight residual 108.68 179.10 -70.42 3.00e+00 1.11e-01 5.51e+02 angle pdb=" F3 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 109.63 179.93 -70.30 3.00e+00 1.11e-01 5.49e+02 angle pdb=" C5 PCW A1107 " pdb=" N PCW A1107 " pdb=" C8 PCW A1107 " ideal model delta sigma weight residual 111.64 86.42 25.22 3.00e+00 1.11e-01 7.06e+01 angle pdb=" C6 PCW A1107 " pdb=" N PCW A1107 " pdb=" C8 PCW A1107 " ideal model delta sigma weight residual 109.11 85.86 23.25 3.00e+00 1.11e-01 6.01e+01 angle pdb=" C7 PCW A1107 " pdb=" N PCW A1107 " pdb=" C8 PCW A1107 " ideal model delta sigma weight residual 108.24 86.95 21.29 3.00e+00 1.11e-01 5.04e+01 ... (remaining 14333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.37: 6249 33.37 - 66.74: 357 66.74 - 100.11: 38 100.11 - 133.48: 40 133.48 - 166.85: 3 Dihedral angle restraints: 6687 sinusoidal: 3074 harmonic: 3613 Sorted by residual: dihedral pdb=" C2' ADP A1103 " pdb=" C1' ADP A1103 " pdb=" N9 ADP A1103 " pdb=" C4 ADP A1103 " ideal model delta sinusoidal sigma weight residual 91.55 -49.80 141.34 1 2.00e+01 2.50e-03 4.27e+01 dihedral pdb=" O1B ADP A1103 " pdb=" O3A ADP A1103 " pdb=" PB ADP A1103 " pdb=" PA ADP A1103 " ideal model delta sinusoidal sigma weight residual 300.00 168.98 131.02 1 2.00e+01 2.50e-03 3.98e+01 dihedral pdb=" N PCW A1106 " pdb=" C4 PCW A1106 " pdb=" C5 PCW A1106 " pdb=" O4P PCW A1106 " ideal model delta sinusoidal sigma weight residual -66.66 100.19 -166.85 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 6684 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1422 0.061 - 0.122: 193 0.122 - 0.183: 22 0.183 - 0.244: 4 0.244 - 0.305: 2 Chirality restraints: 1643 Sorted by residual: chirality pdb=" C51 Q7G A1113 " pdb=" C41 Q7G A1113 " pdb=" C61 Q7G A1113 " pdb=" O51 Q7G A1113 " both_signs ideal model delta sigma weight residual False -2.21 -2.52 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" C2 PCW A1108 " pdb=" C1 PCW A1108 " pdb=" C3 PCW A1108 " pdb=" O2 PCW A1108 " both_signs ideal model delta sigma weight residual False -2.32 -2.58 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" C13 CLR A1109 " pdb=" C12 CLR A1109 " pdb=" C14 CLR A1109 " pdb=" C17 CLR A1109 " both_signs ideal model delta sigma weight residual False -2.93 -2.69 -0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 1640 not shown) Planarity restraints: 1753 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 Q7G B 404 " 0.009 2.00e-02 2.50e+03 1.73e-01 3.73e+02 pdb=" C13 Q7G B 404 " 0.116 2.00e-02 2.50e+03 pdb=" C14 Q7G B 404 " 0.252 2.00e-02 2.50e+03 pdb=" C15 Q7G B 404 " -0.206 2.00e-02 2.50e+03 pdb=" C16 Q7G B 404 " -0.171 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 401 " -0.176 2.00e-02 2.50e+03 1.45e-01 2.65e+02 pdb=" C7 NAG B 401 " 0.047 2.00e-02 2.50e+03 pdb=" C8 NAG B 401 " -0.129 2.00e-02 2.50e+03 pdb=" N2 NAG B 401 " 0.236 2.00e-02 2.50e+03 pdb=" O7 NAG B 401 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C18 PCW A1106 " 0.131 2.00e-02 2.50e+03 1.35e-01 1.83e+02 pdb=" C19 PCW A1106 " -0.117 2.00e-02 2.50e+03 pdb=" C20 PCW A1106 " -0.153 2.00e-02 2.50e+03 pdb=" C21 PCW A1106 " 0.139 2.00e-02 2.50e+03 ... (remaining 1750 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 47 2.45 - 3.06: 6433 3.06 - 3.67: 15308 3.67 - 4.29: 24672 4.29 - 4.90: 41008 Nonbonded interactions: 87468 Sorted by model distance: nonbonded pdb=" F3 ALF A1101 " pdb="MG MG A1102 " model vdw 1.836 2.120 nonbonded pdb=" OD1 ASP A 729 " pdb="MG MG A1102 " model vdw 1.975 2.170 nonbonded pdb=" O THR A 390 " pdb="MG MG A1102 " model vdw 2.088 2.170 nonbonded pdb=" F2 ALF A1101 " pdb=" O HOH A1201 " model vdw 2.162 2.990 nonbonded pdb=" O ILE A 169 " pdb=" OG SER A 172 " model vdw 2.174 3.040 ... (remaining 87463 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.450 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.600 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 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 : 0.008 0.607 10577 Z= 0.657 Angle : 1.260 70.417 14347 Z= 0.471 Chirality : 0.046 0.305 1643 Planarity : 0.008 0.173 1752 Dihedral : 22.332 166.853 4356 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.82 % Allowed : 20.39 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.24), residues: 1242 helix: 1.20 (0.23), residues: 543 sheet: 0.20 (0.44), residues: 125 loop : -0.28 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 442 TYR 0.014 0.001 TYR A 328 PHE 0.024 0.001 PHE A 128 TRP 0.013 0.001 TRP A 968 HIS 0.004 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.29 (10572) covalent geometry : angle 1.26014 / 0.47 (14338) SS BOND : bond 0.00087 / 0.05 ( 3) SS BOND : angle 0.84447 / 0.55 ( 6) hydrogen bonds : bond 0.16979 / 11.26 ( 482) hydrogen bonds : angle 6.61846 / 4.62 ( 1401) Misc. bond : bond 0.60703 / 31.95 ( 1) link_NAG-ASN : bond 0.00267 / 0.14 ( 1) link_NAG-ASN : angle 1.21361 / 0.66 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 98 time to evaluate : 0.372 Fit side-chains REVERT: A 688 GLU cc_start: 0.7739 (mp0) cc_final: 0.7355 (mp0) outliers start: 41 outliers final: 36 residues processed: 138 average time/residue: 0.4783 time to fit residues: 71.2951 Evaluate side-chains 131 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 95 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 134 ASN Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 734 SER Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 141 HIS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 179 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.0070 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 123 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 540 GLN A 887 GLN B 84 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.150307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.115056 restraints weight = 10625.932| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.47 r_work: 0.3188 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.0755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10577 Z= 0.129 Angle : 0.858 31.330 14347 Z= 0.354 Chirality : 0.045 0.259 1643 Planarity : 0.004 0.051 1752 Dihedral : 17.990 170.847 2055 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.45 % Allowed : 18.99 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.24), residues: 1242 helix: 1.32 (0.23), residues: 562 sheet: 0.30 (0.43), residues: 121 loop : -0.27 (0.25), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 442 TYR 0.017 0.001 TYR A 805 PHE 0.013 0.001 PHE A1021 TRP 0.013 0.001 TRP A 968 HIS 0.004 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (10572) covalent geometry : angle 0.85844 / 0.35 (14338) SS BOND : bond 0.00095 / 0.05 ( 3) SS BOND : angle 0.79443 / 0.43 ( 6) hydrogen bonds : bond 0.04218 / 2.80 ( 482) hydrogen bonds : angle 4.81978 / 3.43 ( 1401) Misc. bond : bond 0.00139 / 0.07 ( 1) link_NAG-ASN : bond 0.00930 / 0.49 ( 1) link_NAG-ASN : angle 1.07935 / 0.74 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 110 time to evaluate : 0.434 Fit side-chains REVERT: A 206 LYS cc_start: 0.8062 (mtmm) cc_final: 0.6790 (mptp) REVERT: A 263 GLU cc_start: 0.8088 (pt0) cc_final: 0.7550 (pt0) REVERT: A 520 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8150 (pttt) REVERT: A 853 LYS cc_start: 0.8028 (mttt) cc_final: 0.7674 (mtpt) outliers start: 37 outliers final: 21 residues processed: 141 average time/residue: 0.6237 time to fit residues: 94.6229 Evaluate side-chains 118 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 97 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 65 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 114 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 chunk 56 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 82 GLN B 84 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.149927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.114496 restraints weight = 10691.215| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.47 r_work: 0.3181 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10577 Z= 0.126 Angle : 0.808 30.760 14347 Z= 0.335 Chirality : 0.045 0.260 1643 Planarity : 0.004 0.055 1752 Dihedral : 14.704 165.789 2025 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.98 % Allowed : 20.02 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.23), residues: 1242 helix: 1.48 (0.23), residues: 558 sheet: 0.22 (0.42), residues: 121 loop : -0.29 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 442 TYR 0.020 0.001 TYR A 805 PHE 0.012 0.001 PHE B 264 TRP 0.013 0.001 TRP A 968 HIS 0.005 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (10572) covalent geometry : angle 0.80797 / 0.34 (14338) SS BOND : bond 0.00078 / 0.04 ( 3) SS BOND : angle 0.80696 / 0.48 ( 6) hydrogen bonds : bond 0.04124 / 2.73 ( 482) hydrogen bonds : angle 4.58796 / 3.29 ( 1401) Misc. bond : bond 0.00061 / 0.03 ( 1) link_NAG-ASN : bond 0.00221 / 0.12 ( 1) link_NAG-ASN : angle 1.10038 / 0.67 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.497 Fit side-chains REVERT: A 206 LYS cc_start: 0.8022 (mtmm) cc_final: 0.6765 (mptp) REVERT: A 216 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.6185 (tmm160) REVERT: A 263 GLU cc_start: 0.8080 (pt0) cc_final: 0.7577 (pt0) outliers start: 32 outliers final: 19 residues processed: 126 average time/residue: 0.6335 time to fit residues: 86.0782 Evaluate side-chains 120 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 141 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 81 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 123 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 68 optimal weight: 0.2980 chunk 38 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 GLN A 407 ASN B 82 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.149587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.113985 restraints weight = 10743.784| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.48 r_work: 0.3172 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10577 Z= 0.131 Angle : 0.799 30.977 14347 Z= 0.334 Chirality : 0.045 0.372 1643 Planarity : 0.004 0.054 1752 Dihedral : 12.867 158.572 2021 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.35 % Allowed : 19.27 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.23), residues: 1242 helix: 1.46 (0.22), residues: 564 sheet: 0.21 (0.43), residues: 121 loop : -0.31 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 442 TYR 0.020 0.001 TYR A 805 PHE 0.013 0.001 PHE A1021 TRP 0.013 0.001 TRP A 968 HIS 0.005 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (10572) covalent geometry : angle 0.79924 / 0.33 (14338) SS BOND : bond 0.00106 / 0.05 ( 3) SS BOND : angle 0.81557 / 0.50 ( 6) hydrogen bonds : bond 0.03993 / 2.65 ( 482) hydrogen bonds : angle 4.47636 / 3.22 ( 1401) Misc. bond : bond 0.00045 / 0.02 ( 1) link_NAG-ASN : bond 0.00159 / 0.08 ( 1) link_NAG-ASN : angle 1.05424 / 0.67 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 103 time to evaluate : 0.395 Fit side-chains REVERT: A 206 LYS cc_start: 0.8070 (mtmm) cc_final: 0.6794 (mptp) REVERT: A 216 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.6074 (tmm160) REVERT: A 226 ASP cc_start: 0.8637 (t70) cc_final: 0.8379 (t70) REVERT: A 263 GLU cc_start: 0.8080 (pt0) cc_final: 0.7602 (pt0) REVERT: A 480 MET cc_start: 0.7514 (mmm) cc_final: 0.7152 (mpm) outliers start: 36 outliers final: 22 residues processed: 132 average time/residue: 0.6007 time to fit residues: 85.6758 Evaluate side-chains 120 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 141 HIS Chi-restraints excluded: chain B residue 219 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 95 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 407 ASN A 551 HIS A 689 GLN A 887 GLN A 999 GLN B 82 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.146784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.111230 restraints weight = 10721.624| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.47 r_work: 0.3131 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10577 Z= 0.198 Angle : 0.847 32.267 14347 Z= 0.364 Chirality : 0.048 0.363 1643 Planarity : 0.005 0.051 1752 Dihedral : 13.117 157.269 2021 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.72 % Allowed : 18.90 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.23), residues: 1242 helix: 1.25 (0.22), residues: 563 sheet: 0.04 (0.43), residues: 124 loop : -0.43 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 442 TYR 0.029 0.002 TYR A 805 PHE 0.018 0.002 PHE A1021 TRP 0.016 0.002 TRP A 968 HIS 0.008 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 (10572) covalent geometry : angle 0.84666 / 0.36 (14338) SS BOND : bond 0.00249 / 0.13 ( 3) SS BOND : angle 1.24106 / 0.76 ( 6) hydrogen bonds : bond 0.04882 / 3.26 ( 482) hydrogen bonds : angle 4.71110 / 3.39 ( 1401) Misc. bond : bond 0.00043 / 0.02 ( 1) link_NAG-ASN : bond 0.00139 / 0.07 ( 1) link_NAG-ASN : angle 1.15440 / 0.81 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 101 time to evaluate : 0.487 Fit side-chains REVERT: A 154 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8199 (mp) REVERT: A 204 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7338 (mt-10) REVERT: A 216 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.6236 (tmm160) REVERT: A 263 GLU cc_start: 0.8108 (pt0) cc_final: 0.7618 (pt0) REVERT: A 480 MET cc_start: 0.7570 (mmm) cc_final: 0.7105 (mpm) REVERT: B 177 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8582 (mm) outliers start: 40 outliers final: 24 residues processed: 135 average time/residue: 0.6046 time to fit residues: 88.2985 Evaluate side-chains 126 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 125 ASP Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 177 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 7 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 98 optimal weight: 0.0670 chunk 115 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 58 optimal weight: 0.0070 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 407 ASN A 551 HIS A 999 GLN B 82 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.150684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.115132 restraints weight = 10769.809| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.48 r_work: 0.3187 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10577 Z= 0.104 Angle : 0.768 30.627 14347 Z= 0.321 Chirality : 0.043 0.270 1643 Planarity : 0.004 0.056 1752 Dihedral : 12.338 144.102 2021 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.07 % Allowed : 19.18 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.24), residues: 1242 helix: 1.55 (0.23), residues: 564 sheet: 0.12 (0.43), residues: 121 loop : -0.30 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 442 TYR 0.015 0.001 TYR A 805 PHE 0.011 0.001 PHE B 264 TRP 0.013 0.001 TRP A 968 HIS 0.006 0.001 HIS A 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (10572) covalent geometry : angle 0.76781 / 0.32 (14338) SS BOND : bond 0.00045 / 0.02 ( 3) SS BOND : angle 0.66400 / 0.39 ( 6) hydrogen bonds : bond 0.03544 / 2.35 ( 482) hydrogen bonds : angle 4.36916 / 3.16 ( 1401) Misc. bond : bond 0.00057 / 0.03 ( 1) link_NAG-ASN : bond 0.00364 / 0.19 ( 1) link_NAG-ASN : angle 1.23787 / 0.72 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 108 time to evaluate : 0.405 Fit side-chains REVERT: A 204 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7236 (mt-10) REVERT: A 206 LYS cc_start: 0.8071 (mtmm) cc_final: 0.6813 (mptp) REVERT: A 216 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.6066 (tmm160) REVERT: A 246 GLU cc_start: 0.7704 (mp0) cc_final: 0.7476 (pm20) REVERT: A 263 GLU cc_start: 0.8037 (pt0) cc_final: 0.7561 (pt0) REVERT: A 480 MET cc_start: 0.7656 (mmm) cc_final: 0.7216 (mpm) outliers start: 33 outliers final: 20 residues processed: 135 average time/residue: 0.6170 time to fit residues: 89.9068 Evaluate side-chains 119 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 141 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 76 optimal weight: 1.9990 chunk 58 optimal weight: 0.0470 chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 0.0070 chunk 18 optimal weight: 0.3980 chunk 23 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 4 optimal weight: 0.1980 chunk 20 optimal weight: 0.6980 overall best weight: 0.2296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 407 ASN ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 999 GLN B 82 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.153140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.117884 restraints weight = 10635.272| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.47 r_work: 0.3223 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10577 Z= 0.089 Angle : 0.748 30.091 14347 Z= 0.309 Chirality : 0.042 0.189 1643 Planarity : 0.004 0.058 1752 Dihedral : 11.728 133.778 2017 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.51 % Allowed : 19.65 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.24), residues: 1242 helix: 1.75 (0.23), residues: 565 sheet: 0.07 (0.42), residues: 121 loop : -0.22 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 442 TYR 0.012 0.001 TYR A 805 PHE 0.020 0.001 PHE A 128 TRP 0.011 0.001 TRP A 968 HIS 0.008 0.001 HIS A 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.09 (10572) covalent geometry : angle 0.74790 / 0.31 (14338) SS BOND : bond 0.00035 / 0.02 ( 3) SS BOND : angle 0.59833 / 0.34 ( 6) hydrogen bonds : bond 0.03139 / 2.07 ( 482) hydrogen bonds : angle 4.18042 / 3.03 ( 1401) Misc. bond : bond 0.00045 / 0.02 ( 1) link_NAG-ASN : bond 0.00400 / 0.21 ( 1) link_NAG-ASN : angle 1.28049 / 0.76 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.430 Fit side-chains REVERT: A 165 LYS cc_start: 0.7873 (mptp) cc_final: 0.6922 (mmtt) REVERT: A 204 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7186 (mt-10) REVERT: A 206 LYS cc_start: 0.8037 (mtmm) cc_final: 0.6806 (mptp) REVERT: A 216 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.6022 (tmm160) REVERT: A 246 GLU cc_start: 0.7600 (mp0) cc_final: 0.7376 (pm20) REVERT: A 263 GLU cc_start: 0.8004 (pt0) cc_final: 0.7561 (pt0) REVERT: A 480 MET cc_start: 0.7739 (mmm) cc_final: 0.7254 (mpm) REVERT: B 177 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8513 (mm) outliers start: 27 outliers final: 16 residues processed: 129 average time/residue: 0.5960 time to fit residues: 82.8284 Evaluate side-chains 121 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 141 HIS Chi-restraints excluded: chain B residue 177 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 2 optimal weight: 0.0770 chunk 67 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 GLN A 407 ASN ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 999 GLN B 82 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.150372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.114596 restraints weight = 10631.603| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.48 r_work: 0.3177 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10577 Z= 0.126 Angle : 0.775 30.929 14347 Z= 0.326 Chirality : 0.044 0.176 1643 Planarity : 0.004 0.056 1752 Dihedral : 11.829 131.477 2016 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.42 % Allowed : 20.20 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.24), residues: 1242 helix: 1.64 (0.23), residues: 565 sheet: 0.14 (0.42), residues: 121 loop : -0.23 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 442 TYR 0.021 0.001 TYR A 805 PHE 0.024 0.002 PHE A 128 TRP 0.012 0.001 TRP A 968 HIS 0.009 0.001 HIS A 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (10572) covalent geometry : angle 0.77512 / 0.33 (14338) SS BOND : bond 0.00113 / 0.06 ( 3) SS BOND : angle 0.81063 / 0.50 ( 6) hydrogen bonds : bond 0.03791 / 2.52 ( 482) hydrogen bonds : angle 4.31418 / 3.11 ( 1401) Misc. bond : bond 0.00012 / 0.01 ( 1) link_NAG-ASN : bond 0.00158 / 0.08 ( 1) link_NAG-ASN : angle 1.10053 / 0.66 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.336 Fit side-chains REVERT: A 165 LYS cc_start: 0.7880 (mptp) cc_final: 0.6925 (mmtt) REVERT: A 204 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7239 (mt-10) REVERT: A 206 LYS cc_start: 0.8106 (mtmm) cc_final: 0.6842 (mptp) REVERT: A 216 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.6078 (tmm160) REVERT: A 263 GLU cc_start: 0.8077 (pt0) cc_final: 0.7620 (pt0) REVERT: A 480 MET cc_start: 0.7758 (mmm) cc_final: 0.7379 (mpm) REVERT: A 688 GLU cc_start: 0.8044 (mp0) cc_final: 0.7680 (mp0) REVERT: B 177 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8522 (mm) outliers start: 26 outliers final: 18 residues processed: 131 average time/residue: 0.5958 time to fit residues: 84.2013 Evaluate side-chains 125 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 759 ASP Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 141 HIS Chi-restraints excluded: chain B residue 177 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 52 optimal weight: 0.0060 chunk 34 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 407 ASN ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 999 GLN B 82 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.150674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.115014 restraints weight = 10631.897| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.47 r_work: 0.3183 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10577 Z= 0.116 Angle : 0.770 30.673 14347 Z= 0.322 Chirality : 0.043 0.162 1643 Planarity : 0.004 0.056 1752 Dihedral : 11.626 130.123 2016 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.05 % Allowed : 20.76 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.24), residues: 1242 helix: 1.65 (0.23), residues: 565 sheet: 0.13 (0.42), residues: 121 loop : -0.22 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 442 TYR 0.019 0.001 TYR A 805 PHE 0.024 0.001 PHE A 128 TRP 0.013 0.001 TRP A 968 HIS 0.008 0.001 HIS A 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (10572) covalent geometry : angle 0.77029 / 0.32 (14338) SS BOND : bond 0.00079 / 0.04 ( 3) SS BOND : angle 0.73745 / 0.45 ( 6) hydrogen bonds : bond 0.03660 / 2.43 ( 482) hydrogen bonds : angle 4.28354 / 3.09 ( 1401) Misc. bond : bond 0.00039 / 0.02 ( 1) link_NAG-ASN : bond 0.00247 / 0.13 ( 1) link_NAG-ASN : angle 1.13658 / 0.67 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.399 Fit side-chains REVERT: A 165 LYS cc_start: 0.7857 (mptp) cc_final: 0.6914 (mmtt) REVERT: A 204 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7247 (mt-10) REVERT: A 206 LYS cc_start: 0.8088 (mtmm) cc_final: 0.6833 (mptp) REVERT: A 216 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.6061 (tmm160) REVERT: A 246 GLU cc_start: 0.7717 (mp0) cc_final: 0.7481 (pm20) REVERT: A 263 GLU cc_start: 0.8068 (pt0) cc_final: 0.7611 (pt0) REVERT: A 480 MET cc_start: 0.7770 (mmm) cc_final: 0.7271 (mpm) REVERT: B 177 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8511 (mm) outliers start: 22 outliers final: 16 residues processed: 130 average time/residue: 0.5649 time to fit residues: 79.3190 Evaluate side-chains 123 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 759 ASP Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 177 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 44 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 41 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 0.0470 chunk 43 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 4 optimal weight: 0.4980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 407 ASN ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 689 GLN A 999 GLN B 82 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.151294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.115787 restraints weight = 10571.831| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.47 r_work: 0.3194 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10577 Z= 0.111 Angle : 0.761 30.605 14347 Z= 0.318 Chirality : 0.043 0.161 1643 Planarity : 0.004 0.058 1752 Dihedral : 10.921 129.829 2016 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.96 % Allowed : 20.95 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.24), residues: 1242 helix: 1.68 (0.23), residues: 565 sheet: 0.16 (0.42), residues: 121 loop : -0.23 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 442 TYR 0.017 0.001 TYR A 805 PHE 0.025 0.001 PHE A 128 TRP 0.012 0.001 TRP A 968 HIS 0.009 0.001 HIS A 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (10572) covalent geometry : angle 0.76106 / 0.32 (14338) SS BOND : bond 0.00071 / 0.04 ( 3) SS BOND : angle 0.70297 / 0.43 ( 6) hydrogen bonds : bond 0.03566 / 2.37 ( 482) hydrogen bonds : angle 4.24359 / 3.07 ( 1401) Misc. bond : bond 0.00002 / 0.00 ( 1) link_NAG-ASN : bond 0.00257 / 0.14 ( 1) link_NAG-ASN : angle 1.20290 / 0.72 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.346 Fit side-chains REVERT: A 165 LYS cc_start: 0.7854 (mptp) cc_final: 0.6906 (mmtt) REVERT: A 204 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7234 (mt-10) REVERT: A 206 LYS cc_start: 0.8096 (mtmm) cc_final: 0.6861 (mptp) REVERT: A 216 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.6076 (tmm160) REVERT: A 263 GLU cc_start: 0.8063 (pt0) cc_final: 0.7620 (pt0) REVERT: A 480 MET cc_start: 0.7776 (mmm) cc_final: 0.7283 (mpm) REVERT: A 688 GLU cc_start: 0.7995 (mp0) cc_final: 0.7667 (mp0) REVERT: B 177 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8508 (mm) outliers start: 21 outliers final: 17 residues processed: 125 average time/residue: 0.6019 time to fit residues: 81.0280 Evaluate side-chains 121 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 759 ASP Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 177 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 49 optimal weight: 1.9990 chunk 43 optimal weight: 0.0870 chunk 69 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 4 optimal weight: 0.0980 chunk 14 optimal weight: 0.5980 overall best weight: 0.4760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 407 ASN A 551 HIS ** A 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 999 GLN B 82 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.151603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.116099 restraints weight = 10679.493| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.48 r_work: 0.3198 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10577 Z= 0.104 Angle : 0.751 30.465 14347 Z= 0.314 Chirality : 0.042 0.162 1643 Planarity : 0.004 0.056 1752 Dihedral : 10.813 129.510 2016 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.96 % Allowed : 20.76 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.24), residues: 1242 helix: 1.70 (0.23), residues: 565 sheet: 0.16 (0.42), residues: 121 loop : -0.21 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 442 TYR 0.017 0.001 TYR A 805 PHE 0.025 0.001 PHE A 128 TRP 0.012 0.001 TRP A 968 HIS 0.005 0.001 HIS A 551 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 (10572) covalent geometry : angle 0.75077 / 0.31 (14338) SS BOND : bond 0.00062 / 0.03 ( 3) SS BOND : angle 0.67582 / 0.42 ( 6) hydrogen bonds : bond 0.03505 / 2.32 ( 482) hydrogen bonds : angle 4.20953 / 3.04 ( 1401) Misc. bond : bond 0.00050 / 0.03 ( 1) link_NAG-ASN : bond 0.00283 / 0.15 ( 1) link_NAG-ASN : angle 1.21157 / 0.72 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3918.49 seconds wall clock time: 67 minutes 36.18 seconds (4056.18 seconds total)