Starting phenix.real_space_refine on Sat Sep 12 05:58:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7s7c_24883/09_2026/7s7c_24883.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s7c_24883/09_2026/7s7c_24883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7s7c_24883/09_2026/7s7c_24883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s7c_24883/09_2026/7s7c_24883.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7s7c_24883/09_2026/7s7c_24883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s7c_24883/09_2026/7s7c_24883.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7s7c_24883/09_2026/7s7c_24883.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7s7c_24883/09_2026/7s7c_24883.cif" } resolution = 3.62 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= 0.001 sd= 1.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 34 5.49 5 S 73 5.16 5 C 8696 2.51 5 N 2374 2.21 5 O 2672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13850 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 924, 7376 Classifications: {'peptide': 924} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 41, 'TRANS': 882} Chain breaks: 2 Chain: "B" Number of atoms: 2666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2666 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 22, 'TRANS': 307} Chain breaks: 4 Chain: "C" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 644 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "D" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 574 Classifications: {'RNAv2': 27} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 13, 'rna3p_pyr': 5} Link IDs: {'rna2p': 8, 'rna3p': 18} Unresolved chain links: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 212 Classifications: {'RNAv2': 10} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 5} Link IDs: {'rna3p': 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1166 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 12, 'TRANS': 134} Chain breaks: 2 Chain: "F" Number of atoms: 1211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1211 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 7, 'TRANS': 141} Chain breaks: 2 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8616 SG CYS B 229 55.471 71.347 93.313 1.00150.17 S ATOM 8641 SG CYS B 232 58.103 69.641 91.184 1.00149.28 S ATOM 8719 SG CYS B 242 58.999 72.151 93.729 1.00145.26 S Time building chain proxies: 2.42, per 1000 atoms: 0.17 Number of scatterers: 13850 At special positions: 0 Unit cell: (129.8, 135.3, 154, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 73 16.00 P 34 15.00 O 2672 8.00 N 2374 7.00 C 8696 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 473.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 900 " pdb="ZN ZN B 900 " - pdb=" NE2 HIS B 237 " pdb="ZN ZN B 900 " - pdb=" SG CYS B 242 " pdb="ZN ZN B 900 " - pdb=" SG CYS B 232 " pdb="ZN ZN B 900 " - pdb=" SG CYS B 229 " Number of angles added : 3 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3090 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 12 sheets defined 46.2% alpha, 11.0% beta 8 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 141 through 153 removed outlier: 3.550A pdb=" N ASN A 153 " --> pdb=" O GLN A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 166 removed outlier: 3.749A pdb=" N GLY A 166 " --> pdb=" O THR A 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 163 through 166' Processing helix chain 'A' and resid 167 through 181 removed outlier: 3.975A pdb=" N ALA A 171 " --> pdb=" O LYS A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 207 Processing helix chain 'A' and resid 229 through 238 Processing helix chain 'A' and resid 240 through 245 removed outlier: 3.752A pdb=" N MET A 243 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU A 245 " --> pdb=" O VAL A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 259 removed outlier: 3.706A pdb=" N ARG A 258 " --> pdb=" O HIS A 255 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP A 259 " --> pdb=" O TYR A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 273 Processing helix chain 'A' and resid 288 through 301 removed outlier: 3.856A pdb=" N PHE A 292 " --> pdb=" O ASN A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 356 removed outlier: 3.540A pdb=" N PHE A 343 " --> pdb=" O ARG A 339 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU A 356 " --> pdb=" O ASP A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 397 through 406 removed outlier: 3.778A pdb=" N MET A 406 " --> pdb=" O TYR A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 429 Processing helix chain 'A' and resid 432 through 437 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 444 through 450 removed outlier: 3.550A pdb=" N ARG A 450 " --> pdb=" O PRO A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 474 Processing helix chain 'A' and resid 483 through 488 removed outlier: 3.910A pdb=" N MET A 487 " --> pdb=" O THR A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 522 Processing helix chain 'A' and resid 544 through 553 removed outlier: 4.347A pdb=" N GLN A 550 " --> pdb=" O THR A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 576 Processing helix chain 'A' and resid 580 through 587 removed outlier: 3.745A pdb=" N MET A 584 " --> pdb=" O ASN A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 596 Processing helix chain 'A' and resid 597 through 615 removed outlier: 3.659A pdb=" N ILE A 615 " --> pdb=" O GLN A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 645 Processing helix chain 'A' and resid 646 through 651 removed outlier: 3.898A pdb=" N LEU A 651 " --> pdb=" O PRO A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 708 Processing helix chain 'A' and resid 709 through 713 removed outlier: 3.896A pdb=" N GLU A 713 " --> pdb=" O SER A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 769 removed outlier: 3.710A pdb=" N ARG A 756 " --> pdb=" O PRO A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 807 removed outlier: 3.787A pdb=" N LYS A 791 " --> pdb=" O ASP A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 812 removed outlier: 3.740A pdb=" N ASP A 812 " --> pdb=" O PRO A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 842 removed outlier: 3.524A pdb=" N TYR A 819 " --> pdb=" O LEU A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 862 Processing helix chain 'A' and resid 871 through 880 removed outlier: 4.123A pdb=" N GLU A 879 " --> pdb=" O ARG A 875 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE A 880 " --> pdb=" O VAL A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 895 removed outlier: 3.539A pdb=" N LEU A 888 " --> pdb=" O ASP A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 910 Processing helix chain 'A' and resid 928 through 948 removed outlier: 3.959A pdb=" N LEU A 932 " --> pdb=" O LEU A 928 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN A 934 " --> pdb=" O GLY A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 960 Processing helix chain 'A' and resid 966 through 974 Processing helix chain 'A' and resid 978 through 984 removed outlier: 3.908A pdb=" N ILE A 982 " --> pdb=" O THR A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1015 removed outlier: 3.606A pdb=" N ILE A 993 " --> pdb=" O PHE A 989 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY A1015 " --> pdb=" O ALA A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1030 Processing helix chain 'A' and resid 1033 through 1037 Processing helix chain 'B' and resid 67 through 75 Processing helix chain 'B' and resid 76 through 78 No H-bonds generated for 'chain 'B' and resid 76 through 78' Processing helix chain 'B' and resid 102 through 107 Processing helix chain 'B' and resid 108 through 128 Processing helix chain 'B' and resid 156 through 166 Processing helix chain 'B' and resid 191 through 195 Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 277 through 281 removed outlier: 3.851A pdb=" N GLU B 280 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 300 removed outlier: 3.628A pdb=" N GLY B 300 " --> pdb=" O GLN B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 317 removed outlier: 4.247A pdb=" N ARG B 312 " --> pdb=" O PRO B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 326 removed outlier: 4.225A pdb=" N GLU B 325 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA B 326 " --> pdb=" O TRP B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 403 removed outlier: 3.505A pdb=" N TYR B 402 " --> pdb=" O VAL B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 667 removed outlier: 3.680A pdb=" N PHE B 666 " --> pdb=" O ASP B 662 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA B 667 " --> pdb=" O MET B 663 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 662 through 667' Processing helix chain 'B' and resid 683 through 692 Processing helix chain 'B' and resid 695 through 702 Processing helix chain 'C' and resid 22 through 32 removed outlier: 4.030A pdb=" N GLN C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 70 Processing helix chain 'E' and resid 633 through 645 Processing helix chain 'E' and resid 646 through 651 Processing helix chain 'E' and resid 652 through 654 No H-bonds generated for 'chain 'E' and resid 652 through 654' Processing helix chain 'E' and resid 752 through 770 removed outlier: 3.626A pdb=" N ARG E 756 " --> pdb=" O PRO E 752 " (cutoff:3.500A) Processing helix chain 'E' and resid 787 through 799 Processing helix chain 'F' and resid 57 through 72 Processing helix chain 'F' and resid 102 through 127 removed outlier: 5.742A pdb=" N GLN F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLU F 111 " --> pdb=" O GLN F 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 99 through 103 removed outlier: 6.487A pdb=" N VAL A 249 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N LEU A 282 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N PHE A 251 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A 186 " --> pdb=" O TRP A 248 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL A 185 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N MET A 227 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N PHE A 187 " --> pdb=" O MET A 227 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 453 through 455 removed outlier: 6.669A pdb=" N GLY A 453 " --> pdb=" O PHE A 480 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL A 496 " --> pdb=" O ILE A 536 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N MET A 538 " --> pdb=" O VAL A 496 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N PHE A 498 " --> pdb=" O MET A 538 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU A 328 " --> pdb=" O TYR B 336 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 502 through 504 Processing sheet with id=AA4, first strand: chain 'A' and resid 667 through 673 removed outlier: 6.591A pdb=" N VAL A 662 " --> pdb=" O PHE A 669 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N TRP A 671 " --> pdb=" O VAL A 660 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL A 660 " --> pdb=" O TRP A 671 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL A 673 " --> pdb=" O ARG A 658 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ARG A 658 " --> pdb=" O VAL A 673 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LEU A 659 " --> pdb=" O ILE A 739 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ILE A 739 " --> pdb=" O LEU A 659 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LYS A 661 " --> pdb=" O SER A 737 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 676 through 680 Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.615A pdb=" N PHE B 99 " --> pdb=" O VAL F 169 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL F 169 " --> pdb=" O PHE B 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.615A pdb=" N PHE B 99 " --> pdb=" O VAL F 169 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL F 169 " --> pdb=" O PHE B 99 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 327 through 328 Processing sheet with id=AA9, first strand: chain 'C' and resid 36 through 40 removed outlier: 6.897A pdb=" N ASN C 56 " --> pdb=" O ILE C 37 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL C 39 " --> pdb=" O PHE C 54 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N PHE C 54 " --> pdb=" O VAL C 39 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 74 through 75 Processing sheet with id=AB2, first strand: chain 'E' and resid 727 through 732 removed outlier: 3.562A pdb=" N LEU E 693 " --> pdb=" O LYS E 680 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN E 676 " --> pdb=" O GLU E 697 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LEU E 699 " --> pdb=" O VAL E 674 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL E 674 " --> pdb=" O LEU E 699 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASP E 668 " --> pdb=" O ASN E 664 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ASN E 664 " --> pdb=" O ASP E 668 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY E 670 " --> pdb=" O VAL E 662 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL E 662 " --> pdb=" O GLY E 670 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS E 663 " --> pdb=" O LEU E 736 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N LEU E 736 " --> pdb=" O LYS E 663 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 78 through 79 removed outlier: 3.546A pdb=" N ARG F 79 " --> pdb=" O GLU F 148 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 544 hydrogen bonds defined for protein. 1557 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 24 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 2.52 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4229 1.33 - 1.45: 1916 1.45 - 1.57: 7867 1.57 - 1.69: 68 1.69 - 1.81: 118 Bond restraints: 14198 Sorted by residual: bond pdb=" C3' U D 18 " pdb=" O3' U D 18 " ideal model delta sigma weight residual 1.415 1.436 -0.021 2.00e-02 2.50e+03 1.15e+00 bond pdb=" C5 G D 8 " pdb=" C6 G D 8 " ideal model delta sigma weight residual 1.419 1.403 0.016 2.00e-02 2.50e+03 6.07e-01 bond pdb=" C3' A D 24 " pdb=" O3' A D 24 " ideal model delta sigma weight residual 1.415 1.430 -0.015 2.00e-02 2.50e+03 5.82e-01 bond pdb=" C1' A D 24 " pdb=" N9 A D 24 " ideal model delta sigma weight residual 1.478 1.463 0.015 2.00e-02 2.50e+03 5.42e-01 bond pdb=" N7 G D 6 " pdb=" C5 G D 6 " ideal model delta sigma weight residual 1.388 1.374 0.014 2.00e-02 2.50e+03 4.83e-01 ... (remaining 14193 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 18500 1.08 - 2.16: 595 2.16 - 3.25: 141 3.25 - 4.33: 79 4.33 - 5.41: 15 Bond angle restraints: 19330 Sorted by residual: angle pdb=" C3' U D 18 " pdb=" O3' U D 18 " pdb=" P U D 19 " ideal model delta sigma weight residual 119.70 123.16 -3.46 1.20e+00 6.94e-01 8.30e+00 angle pdb=" C LYS F 160 " pdb=" N ASN F 161 " pdb=" CA ASN F 161 " ideal model delta sigma weight residual 121.54 126.73 -5.19 1.91e+00 2.74e-01 7.38e+00 angle pdb=" C3' A D 24 " pdb=" C2' A D 24 " pdb=" O2' A D 24 " ideal model delta sigma weight residual 109.80 114.81 -5.01 2.00e+00 2.50e-01 6.28e+00 angle pdb=" C3' A D 25 " pdb=" C2' A D 25 " pdb=" O2' A D 25 " ideal model delta sigma weight residual 109.80 114.76 -4.96 2.00e+00 2.50e-01 6.14e+00 angle pdb=" C3' A D 23 " pdb=" C2' A D 23 " pdb=" O2' A D 23 " ideal model delta sigma weight residual 109.80 114.71 -4.91 2.00e+00 2.50e-01 6.03e+00 ... (remaining 19325 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.70: 8434 31.70 - 63.41: 181 63.41 - 95.11: 21 95.11 - 126.81: 0 126.81 - 158.52: 1 Dihedral angle restraints: 8637 sinusoidal: 3884 harmonic: 4753 Sorted by residual: dihedral pdb=" C4' A D 24 " pdb=" C3' A D 24 " pdb=" C2' A D 24 " pdb=" C1' A D 24 " ideal model delta sinusoidal sigma weight residual 36.34 -37.34 73.69 1 3.10e+00 1.04e-01 7.18e+02 dihedral pdb=" C4' A D 25 " pdb=" C3' A D 25 " pdb=" C2' A D 25 " pdb=" C1' A D 25 " ideal model delta sinusoidal sigma weight residual 36.34 -37.17 73.51 1 3.10e+00 1.04e-01 7.15e+02 dihedral pdb=" C4' U D 16 " pdb=" C3' U D 16 " pdb=" C2' U D 16 " pdb=" C1' U D 16 " ideal model delta sinusoidal sigma weight residual 36.34 -36.66 73.00 1 3.10e+00 1.04e-01 7.07e+02 ... (remaining 8634 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1870 0.063 - 0.125: 246 0.125 - 0.188: 10 0.188 - 0.250: 36 0.250 - 0.313: 14 Chirality restraints: 2176 Sorted by residual: chirality pdb=" P U D 19 " pdb=" OP1 U D 19 " pdb=" OP2 U D 19 " pdb=" O5' U D 19 " both_signs ideal model delta sigma weight residual True 2.17 -2.49 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" C2' U D 18 " pdb=" C3' U D 18 " pdb=" O2' U D 18 " pdb=" C1' U D 18 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C2' A D 15 " pdb=" C3' A D 15 " pdb=" O2' A D 15 " pdb=" C1' A D 15 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 2173 not shown) Planarity restraints: 2361 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C D 9 " -0.006 2.00e-02 2.50e+03 1.01e-02 2.29e+00 pdb=" N1 C D 9 " 0.009 2.00e-02 2.50e+03 pdb=" C2 C D 9 " -0.022 2.00e-02 2.50e+03 pdb=" O2 C D 9 " 0.013 2.00e-02 2.50e+03 pdb=" N3 C D 9 " 0.005 2.00e-02 2.50e+03 pdb=" C4 C D 9 " -0.010 2.00e-02 2.50e+03 pdb=" N4 C D 9 " 0.003 2.00e-02 2.50e+03 pdb=" C5 C D 9 " 0.003 2.00e-02 2.50e+03 pdb=" C6 C D 9 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 655 " -0.024 5.00e-02 4.00e+02 3.67e-02 2.16e+00 pdb=" N PRO A 656 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 656 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 656 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A D 26 " 0.020 2.00e-02 2.50e+03 8.44e-03 1.96e+00 pdb=" N9 A D 26 " -0.017 2.00e-02 2.50e+03 pdb=" C8 A D 26 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A D 26 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A D 26 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A D 26 " 0.002 2.00e-02 2.50e+03 pdb=" N6 A D 26 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A D 26 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A D 26 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A D 26 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A D 26 " -0.004 2.00e-02 2.50e+03 ... (remaining 2358 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 186 2.60 - 3.17: 12485 3.17 - 3.75: 20322 3.75 - 4.32: 27806 4.32 - 4.90: 47166 Nonbonded interactions: 107965 Sorted by model distance: nonbonded pdb=" OG SER A 393 " pdb=" OG1 THR A 499 " model vdw 2.019 3.040 nonbonded pdb=" OG SER B 234 " pdb="ZN ZN B 900 " model vdw 2.066 2.230 nonbonded pdb=" OG SER B 695 " pdb=" OD1 ASN B 698 " model vdw 2.079 3.040 nonbonded pdb=" NZ LYS A 192 " pdb=" OD2 ASP A 215 " model vdw 2.110 3.120 nonbonded pdb=" NE2 GLN B 272 " pdb=" O ALA B 276 " model vdw 2.144 3.120 ... (remaining 107960 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 group one per residue 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: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.610 Find NCS groups from input model: 0.060 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 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 0.058 14202 Z= 0.138 Angle : 0.548 6.558 19333 Z= 0.266 Chirality : 0.055 0.313 2176 Planarity : 0.003 0.037 2361 Dihedral : 13.073 158.517 5547 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 1.10 % Allowed : 6.93 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.22), residues: 1599 helix: 1.39 (0.21), residues: 677 sheet: -0.07 (0.49), residues: 125 loop : -2.01 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1005 TYR 0.009 0.001 TYR A 612 PHE 0.011 0.001 PHE C 13 TRP 0.009 0.001 TRP F 198 HIS 0.002 0.001 HIS B 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (14198) covalent geometry : angle 0.54540 / 0.27 (19330) hydrogen bonds : bond 0.13809 / 10.12 ( 568) hydrogen bonds : angle 5.74366 / 4.10 ( 1605) metal coordination : bond 0.03657 / 1.82 ( 4) metal coordination : angle 4.64024 / 2.63 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 294 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8233 (pp) REVERT: A 202 MET cc_start: 0.6643 (mmt) cc_final: 0.6441 (mmt) REVERT: A 207 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7473 (mm-40) REVERT: A 648 LYS cc_start: 0.7189 (ptmt) cc_final: 0.6876 (ttpt) REVERT: A 679 LYS cc_start: 0.7521 (tttt) cc_final: 0.7288 (tttm) REVERT: A 767 GLN cc_start: 0.7096 (tt0) cc_final: 0.6198 (tm-30) REVERT: A 915 GLN cc_start: 0.7463 (mt0) cc_final: 0.7050 (mt0) REVERT: A 973 TRP cc_start: 0.7695 (t-100) cc_final: 0.7357 (t-100) REVERT: A 986 THR cc_start: 0.9196 (t) cc_final: 0.8878 (m) REVERT: B 97 ILE cc_start: 0.8412 (pt) cc_final: 0.8201 (mt) REVERT: B 271 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.7362 (mp10) REVERT: B 671 THR cc_start: 0.8029 (m) cc_final: 0.7779 (p) REVERT: E 642 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7559 (tm-30) REVERT: F 152 LYS cc_start: 0.6845 (mmtp) cc_final: 0.6624 (mmtt) outliers start: 16 outliers final: 9 residues processed: 309 average time/residue: 0.1175 time to fit residues: 52.2956 Evaluate side-chains 202 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 190 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 271 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.0570 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 ASN B 191 ASN B 391 GLN B 698 ASN F 177 ASN ** F 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.152955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.116914 restraints weight = 17921.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.117355 restraints weight = 15124.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.118497 restraints weight = 15315.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.119333 restraints weight = 9879.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.120002 restraints weight = 8648.380| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14202 Z= 0.156 Angle : 0.766 14.845 19333 Z= 0.354 Chirality : 0.066 0.999 2176 Planarity : 0.004 0.048 2361 Dihedral : 11.888 155.969 2194 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.99 % Allowed : 11.74 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.15 (0.22), residues: 1599 helix: 1.57 (0.20), residues: 676 sheet: 0.18 (0.48), residues: 120 loop : -1.71 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 751 TYR 0.022 0.001 TYR E 649 PHE 0.024 0.002 PHE C 52 TRP 0.009 0.001 TRP B 198 HIS 0.004 0.001 HIS A 645 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (14198) covalent geometry : angle 0.76353 / 0.35 (19330) hydrogen bonds : bond 0.04364 / 2.93 ( 568) hydrogen bonds : angle 4.53800 / 3.25 ( 1605) metal coordination : bond 0.01572 / 0.78 ( 4) metal coordination : angle 4.97912 / 2.67 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 212 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8511 (pp) REVERT: A 207 GLN cc_start: 0.7553 (OUTLIER) cc_final: 0.7337 (mm-40) REVERT: A 212 MET cc_start: 0.7339 (mtp) cc_final: 0.6996 (ttm) REVERT: A 333 ASP cc_start: 0.6862 (t0) cc_final: 0.6631 (t0) REVERT: A 679 LYS cc_start: 0.7600 (tttt) cc_final: 0.7399 (tttm) REVERT: A 716 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7586 (ttpp) REVERT: A 767 GLN cc_start: 0.7407 (tt0) cc_final: 0.6457 (tm-30) REVERT: A 1004 LEU cc_start: 0.7844 (tp) cc_final: 0.7397 (tp) REVERT: B 79 ARG cc_start: 0.7985 (ppt170) cc_final: 0.7010 (ppt170) REVERT: B 97 ILE cc_start: 0.8444 (pt) cc_final: 0.8186 (mt) REVERT: B 100 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.8235 (mtp) REVERT: B 126 GLN cc_start: 0.6484 (tm-30) cc_final: 0.5849 (tt0) REVERT: B 313 MET cc_start: 0.5792 (tmm) cc_final: 0.5248 (tmm) REVERT: C 25 LEU cc_start: 0.8183 (mp) cc_final: 0.7608 (tp) REVERT: E 765 GLU cc_start: 0.7518 (tm-30) cc_final: 0.7301 (tm-30) REVERT: E 767 GLN cc_start: 0.7318 (tp40) cc_final: 0.6951 (tp40) REVERT: E 788 GLN cc_start: 0.7463 (tp40) cc_final: 0.6993 (mm-40) REVERT: F 87 ASP cc_start: 0.6331 (p0) cc_final: 0.6059 (p0) REVERT: F 91 ASP cc_start: 0.6362 (m-30) cc_final: 0.6099 (m-30) outliers start: 29 outliers final: 16 residues processed: 228 average time/residue: 0.0988 time to fit residues: 33.9408 Evaluate side-chains 198 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain A residue 716 LYS Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 978 THR Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain E residue 662 VAL Chi-restraints excluded: chain E residue 746 ILE Chi-restraints excluded: chain E residue 774 ILE Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 176 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 66 optimal weight: 7.9990 chunk 121 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 chunk 54 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 156 optimal weight: 0.2980 chunk 106 optimal weight: 0.9980 chunk 131 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 118 ASN B 189 ASN B 699 GLN C 16 ASN F 127 GLN ** F 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 193 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.151359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.115987 restraints weight = 18341.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.115097 restraints weight = 16275.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.116999 restraints weight = 15499.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.118068 restraints weight = 10224.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.118646 restraints weight = 9148.958| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14202 Z= 0.170 Angle : 0.679 10.006 19333 Z= 0.323 Chirality : 0.055 0.805 2176 Planarity : 0.004 0.054 2361 Dihedral : 11.727 166.170 2181 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.02 % Allowed : 12.97 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.21), residues: 1599 helix: 1.45 (0.20), residues: 663 sheet: -0.03 (0.49), residues: 118 loop : -1.68 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 751 TYR 0.026 0.001 TYR E 649 PHE 0.018 0.002 PHE A 893 TRP 0.015 0.002 TRP A 973 HIS 0.003 0.001 HIS A 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (14198) covalent geometry : angle 0.67753 / 0.32 (19330) hydrogen bonds : bond 0.04363 / 2.89 ( 568) hydrogen bonds : angle 4.46040 / 3.20 ( 1605) metal coordination : bond 0.00855 / 0.43 ( 4) metal coordination : angle 4.15923 / 2.21 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 185 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8511 (pp) REVERT: A 212 MET cc_start: 0.7350 (mtp) cc_final: 0.6963 (ttm) REVERT: A 335 ASN cc_start: 0.6848 (m110) cc_final: 0.6525 (t0) REVERT: A 408 LYS cc_start: 0.8426 (ttmt) cc_final: 0.8188 (ttmm) REVERT: A 679 LYS cc_start: 0.7598 (tttt) cc_final: 0.7381 (tttm) REVERT: A 693 LEU cc_start: 0.5893 (OUTLIER) cc_final: 0.5580 (mm) REVERT: A 716 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7637 (ttpp) REVERT: A 767 GLN cc_start: 0.7345 (tt0) cc_final: 0.6447 (tm-30) REVERT: B 79 ARG cc_start: 0.7969 (ppt170) cc_final: 0.6867 (ppt170) REVERT: B 97 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8242 (mt) REVERT: B 126 GLN cc_start: 0.6261 (tm-30) cc_final: 0.5774 (tt0) REVERT: B 313 MET cc_start: 0.5974 (tmm) cc_final: 0.5443 (tmm) REVERT: B 676 GLU cc_start: 0.7549 (tp30) cc_final: 0.6936 (mp0) REVERT: B 701 LYS cc_start: 0.7109 (ptpt) cc_final: 0.6908 (mtmt) REVERT: C 82 ILE cc_start: 0.8113 (mm) cc_final: 0.7846 (mm) REVERT: E 765 GLU cc_start: 0.7586 (tm-30) cc_final: 0.7355 (tm-30) REVERT: E 788 GLN cc_start: 0.7550 (tp40) cc_final: 0.7148 (mm-40) outliers start: 44 outliers final: 26 residues processed: 217 average time/residue: 0.1127 time to fit residues: 36.9831 Evaluate side-chains 192 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 716 LYS Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 978 THR Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 671 THR Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain E residue 662 VAL Chi-restraints excluded: chain E residue 746 ILE Chi-restraints excluded: chain E residue 774 ILE Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 176 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 112 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 59 HIS E 664 ASN ** F 185 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 = 0.3996 r_free = 0.3996 target = 0.154920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.119127 restraints weight = 17985.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.121067 restraints weight = 15397.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.121524 restraints weight = 15060.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.122302 restraints weight = 9425.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.122738 restraints weight = 8234.998| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14202 Z= 0.137 Angle : 0.630 8.373 19333 Z= 0.301 Chirality : 0.052 0.626 2176 Planarity : 0.004 0.055 2361 Dihedral : 11.499 160.411 2178 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.95 % Allowed : 14.76 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.16 (0.21), residues: 1599 helix: 1.53 (0.20), residues: 669 sheet: 0.10 (0.52), residues: 111 loop : -1.62 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1032 TYR 0.024 0.001 TYR E 649 PHE 0.017 0.001 PHE A 893 TRP 0.027 0.002 TRP A 973 HIS 0.005 0.001 HIS C 59 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (14198) covalent geometry : angle 0.62872 / 0.30 (19330) hydrogen bonds : bond 0.03903 / 2.58 ( 568) hydrogen bonds : angle 4.29207 / 3.07 ( 1605) metal coordination : bond 0.01024 / 0.51 ( 4) metal coordination : angle 3.10789 / 1.65 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 177 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8530 (pp) REVERT: A 212 MET cc_start: 0.7354 (mtp) cc_final: 0.6983 (ttm) REVERT: A 679 LYS cc_start: 0.7603 (tttt) cc_final: 0.7390 (tttm) REVERT: A 693 LEU cc_start: 0.5950 (OUTLIER) cc_final: 0.5604 (mm) REVERT: A 767 GLN cc_start: 0.7349 (tt0) cc_final: 0.6424 (tm-30) REVERT: B 79 ARG cc_start: 0.7945 (ppt170) cc_final: 0.6962 (ppt170) REVERT: B 126 GLN cc_start: 0.6087 (tm-30) cc_final: 0.5666 (tt0) REVERT: B 130 ASP cc_start: 0.6760 (OUTLIER) cc_final: 0.6242 (p0) REVERT: B 313 MET cc_start: 0.5935 (tmm) cc_final: 0.5400 (tmm) REVERT: B 676 GLU cc_start: 0.7317 (tp30) cc_final: 0.6792 (mp0) REVERT: B 701 LYS cc_start: 0.7100 (ptpt) cc_final: 0.6742 (mtmt) REVERT: C 25 LEU cc_start: 0.8244 (mp) cc_final: 0.7673 (tp) REVERT: E 639 GLU cc_start: 0.7305 (mm-30) cc_final: 0.6960 (tm-30) REVERT: E 788 GLN cc_start: 0.7587 (tp40) cc_final: 0.7217 (mm-40) outliers start: 43 outliers final: 28 residues processed: 206 average time/residue: 0.1054 time to fit residues: 32.9511 Evaluate side-chains 189 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 978 THR Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain E residue 662 VAL Chi-restraints excluded: chain E residue 746 ILE Chi-restraints excluded: chain E residue 774 ILE Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 176 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 97 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 107 optimal weight: 20.0000 chunk 37 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 HIS ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 HIS E 786 GLN F 177 ASN ** F 185 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 = 0.3939 r_free = 0.3939 target = 0.149441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.114013 restraints weight = 18341.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.112706 restraints weight = 16848.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.114585 restraints weight = 16617.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.115543 restraints weight = 10949.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.116071 restraints weight = 10049.746| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 14202 Z= 0.230 Angle : 0.706 9.393 19333 Z= 0.341 Chirality : 0.053 0.589 2176 Planarity : 0.005 0.064 2361 Dihedral : 11.560 160.178 2178 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.82 % Favored : 93.12 % Rotamer: Outliers : 3.84 % Allowed : 15.65 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.55 (0.21), residues: 1599 helix: 1.12 (0.20), residues: 670 sheet: -0.07 (0.49), residues: 126 loop : -1.79 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 72 TYR 0.025 0.002 TYR E 649 PHE 0.025 0.002 PHE C 13 TRP 0.021 0.002 TRP A 973 HIS 0.003 0.001 HIS E 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.23 (14198) covalent geometry : angle 0.70507 / 0.34 (19330) hydrogen bonds : bond 0.04795 / 3.16 ( 568) hydrogen bonds : angle 4.60918 / 3.33 ( 1605) metal coordination : bond 0.00591 / 0.30 ( 4) metal coordination : angle 3.42105 / 1.81 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 171 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8433 (pp) REVERT: A 212 MET cc_start: 0.7410 (mtp) cc_final: 0.7102 (ttm) REVERT: A 254 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.7701 (pp) REVERT: A 306 VAL cc_start: 0.8654 (OUTLIER) cc_final: 0.8181 (m) REVERT: A 468 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7799 (mt-10) REVERT: A 679 LYS cc_start: 0.7697 (tttt) cc_final: 0.7487 (tttm) REVERT: A 693 LEU cc_start: 0.5820 (OUTLIER) cc_final: 0.5504 (mm) REVERT: A 716 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7501 (ttpt) REVERT: A 767 GLN cc_start: 0.7441 (tt0) cc_final: 0.6510 (tm-30) REVERT: B 79 ARG cc_start: 0.7991 (ppt170) cc_final: 0.6896 (ppt170) REVERT: B 97 ILE cc_start: 0.8550 (pt) cc_final: 0.8303 (mt) REVERT: B 126 GLN cc_start: 0.6127 (tm-30) cc_final: 0.5706 (tt0) REVERT: B 130 ASP cc_start: 0.6747 (OUTLIER) cc_final: 0.6278 (p0) REVERT: B 313 MET cc_start: 0.6200 (tmm) cc_final: 0.5901 (tmm) REVERT: B 676 GLU cc_start: 0.7423 (tp30) cc_final: 0.6815 (pm20) REVERT: C 25 LEU cc_start: 0.8248 (mp) cc_final: 0.7805 (tp) REVERT: E 639 GLU cc_start: 0.7272 (tm-30) cc_final: 0.7071 (mm-30) REVERT: E 788 GLN cc_start: 0.7620 (tp40) cc_final: 0.7248 (mm-40) outliers start: 56 outliers final: 36 residues processed: 208 average time/residue: 0.1086 time to fit residues: 34.4018 Evaluate side-chains 197 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 155 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 566 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 716 LYS Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 948 GLU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 978 THR Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 671 THR Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain E residue 662 VAL Chi-restraints excluded: chain E residue 735 LEU Chi-restraints excluded: chain E residue 746 ILE Chi-restraints excluded: chain E residue 774 ILE Chi-restraints excluded: chain F residue 176 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 68 optimal weight: 9.9990 chunk 121 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 11 optimal weight: 0.0980 chunk 39 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 69 optimal weight: 8.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.156351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.120602 restraints weight = 17807.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.120485 restraints weight = 14923.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.123459 restraints weight = 12652.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.123616 restraints weight = 8784.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.123967 restraints weight = 8990.604| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14202 Z= 0.123 Angle : 0.611 9.207 19333 Z= 0.293 Chirality : 0.049 0.477 2176 Planarity : 0.004 0.067 2361 Dihedral : 11.316 166.349 2178 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.88 % Allowed : 16.27 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.21), residues: 1599 helix: 1.51 (0.20), residues: 669 sheet: 0.04 (0.50), residues: 116 loop : -1.64 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 72 TYR 0.025 0.001 TYR E 649 PHE 0.015 0.001 PHE C 13 TRP 0.017 0.002 TRP A 973 HIS 0.003 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (14198) covalent geometry : angle 0.61034 / 0.29 (19330) hydrogen bonds : bond 0.03662 / 2.42 ( 568) hydrogen bonds : angle 4.25307 / 3.05 ( 1605) metal coordination : bond 0.00559 / 0.28 ( 4) metal coordination : angle 3.00714 / 1.59 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 168 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8460 (pp) REVERT: A 181 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7694 (mm-30) REVERT: A 212 MET cc_start: 0.7335 (mtp) cc_final: 0.7013 (ttm) REVERT: A 254 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.7719 (pp) REVERT: A 306 VAL cc_start: 0.8518 (OUTLIER) cc_final: 0.8017 (m) REVERT: A 679 LYS cc_start: 0.7652 (tttt) cc_final: 0.7228 (tttm) REVERT: A 693 LEU cc_start: 0.5862 (OUTLIER) cc_final: 0.5510 (mm) REVERT: A 767 GLN cc_start: 0.7322 (tt0) cc_final: 0.6373 (tm-30) REVERT: B 79 ARG cc_start: 0.7858 (ppt170) cc_final: 0.6869 (ppt170) REVERT: B 97 ILE cc_start: 0.8645 (pt) cc_final: 0.8252 (mt) REVERT: B 126 GLN cc_start: 0.6112 (tm-30) cc_final: 0.5631 (tt0) REVERT: B 130 ASP cc_start: 0.6764 (OUTLIER) cc_final: 0.6278 (p0) REVERT: B 313 MET cc_start: 0.6027 (tmm) cc_final: 0.5782 (tmm) REVERT: B 676 GLU cc_start: 0.7272 (tp30) cc_final: 0.6760 (pm20) REVERT: C 25 LEU cc_start: 0.8172 (mp) cc_final: 0.7709 (tp) REVERT: E 639 GLU cc_start: 0.7137 (tm-30) cc_final: 0.6892 (tm-30) REVERT: E 788 GLN cc_start: 0.7640 (tp40) cc_final: 0.7232 (mm-40) outliers start: 42 outliers final: 27 residues processed: 200 average time/residue: 0.1112 time to fit residues: 34.1862 Evaluate side-chains 190 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 948 GLU Chi-restraints excluded: chain A residue 953 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 978 THR Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 671 THR Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain E residue 662 VAL Chi-restraints excluded: chain E residue 746 ILE Chi-restraints excluded: chain E residue 774 ILE Chi-restraints excluded: chain F residue 176 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 130 optimal weight: 0.4980 chunk 128 optimal weight: 0.0970 chunk 21 optimal weight: 0.7980 chunk 160 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 150 optimal weight: 0.0020 chunk 36 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 109 HIS B 394 GLN ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 HIS ** F 185 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 = 0.4002 r_free = 0.4002 target = 0.155449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.119433 restraints weight = 17927.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.119908 restraints weight = 15007.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.120742 restraints weight = 15256.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.121783 restraints weight = 9561.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.125266 restraints weight = 8281.316| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14202 Z= 0.108 Angle : 0.592 7.376 19333 Z= 0.283 Chirality : 0.048 0.394 2176 Planarity : 0.004 0.055 2361 Dihedral : 11.165 179.691 2178 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.88 % Allowed : 15.92 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.21), residues: 1599 helix: 1.57 (0.20), residues: 680 sheet: 0.06 (0.50), residues: 114 loop : -1.62 (0.22), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 72 TYR 0.021 0.001 TYR E 649 PHE 0.012 0.001 PHE C 13 TRP 0.029 0.002 TRP A 973 HIS 0.003 0.001 HIS B 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (14198) covalent geometry : angle 0.59117 / 0.28 (19330) hydrogen bonds : bond 0.03332 / 2.21 ( 568) hydrogen bonds : angle 4.04547 / 2.89 ( 1605) metal coordination : bond 0.00417 / 0.21 ( 4) metal coordination : angle 2.53335 / 1.34 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 176 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8439 (pp) REVERT: A 212 MET cc_start: 0.7321 (mtp) cc_final: 0.6964 (ttm) REVERT: A 254 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.7657 (pp) REVERT: A 306 VAL cc_start: 0.8477 (OUTLIER) cc_final: 0.7955 (m) REVERT: A 679 LYS cc_start: 0.7655 (tttt) cc_final: 0.7225 (tttm) REVERT: A 693 LEU cc_start: 0.5876 (OUTLIER) cc_final: 0.5551 (mm) REVERT: A 767 GLN cc_start: 0.7240 (tt0) cc_final: 0.6317 (tm-30) REVERT: B 79 ARG cc_start: 0.7718 (ppt170) cc_final: 0.6772 (ppt170) REVERT: B 97 ILE cc_start: 0.8675 (pt) cc_final: 0.8321 (mt) REVERT: B 126 GLN cc_start: 0.5997 (tm-30) cc_final: 0.5617 (tt0) REVERT: B 130 ASP cc_start: 0.6684 (OUTLIER) cc_final: 0.6200 (p0) REVERT: B 676 GLU cc_start: 0.7204 (tp30) cc_final: 0.6856 (pm20) REVERT: B 701 LYS cc_start: 0.7409 (mtpt) cc_final: 0.6593 (mttp) REVERT: C 25 LEU cc_start: 0.8161 (mp) cc_final: 0.7727 (tp) REVERT: E 757 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.7187 (mm110) REVERT: E 788 GLN cc_start: 0.7594 (tp40) cc_final: 0.7265 (mm-40) REVERT: F 101 ASN cc_start: 0.8070 (t0) cc_final: 0.7731 (t0) outliers start: 42 outliers final: 28 residues processed: 209 average time/residue: 0.1091 time to fit residues: 35.0656 Evaluate side-chains 191 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 953 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 978 THR Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain A residue 1014 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 671 THR Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain E residue 662 VAL Chi-restraints excluded: chain E residue 746 ILE Chi-restraints excluded: chain E residue 757 GLN Chi-restraints excluded: chain E residue 774 ILE Chi-restraints excluded: chain E residue 780 ILE Chi-restraints excluded: chain F residue 176 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 134 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 49 optimal weight: 0.0370 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 56 ASN C 59 HIS F 177 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.155984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.119864 restraints weight = 17722.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.118260 restraints weight = 15299.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.120251 restraints weight = 15286.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.121309 restraints weight = 10313.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.121832 restraints weight = 9147.423| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14202 Z= 0.138 Angle : 0.616 8.907 19333 Z= 0.294 Chirality : 0.048 0.362 2176 Planarity : 0.004 0.051 2361 Dihedral : 11.149 179.073 2178 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.16 % Allowed : 15.99 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.21), residues: 1599 helix: 1.55 (0.20), residues: 669 sheet: 0.08 (0.50), residues: 114 loop : -1.56 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 72 TYR 0.024 0.001 TYR E 649 PHE 0.013 0.001 PHE C 13 TRP 0.025 0.002 TRP A 973 HIS 0.003 0.001 HIS E 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (14198) covalent geometry : angle 0.61581 / 0.29 (19330) hydrogen bonds : bond 0.03640 / 2.39 ( 568) hydrogen bonds : angle 4.11846 / 2.95 ( 1605) metal coordination : bond 0.00376 / 0.19 ( 4) metal coordination : angle 2.04894 / 1.12 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 168 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8473 (pp) REVERT: A 181 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7735 (mm-30) REVERT: A 212 MET cc_start: 0.7334 (mtp) cc_final: 0.7097 (ttm) REVERT: A 254 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.7694 (pp) REVERT: A 306 VAL cc_start: 0.8544 (OUTLIER) cc_final: 0.8316 (p) REVERT: A 679 LYS cc_start: 0.7706 (tttt) cc_final: 0.7267 (tttm) REVERT: A 693 LEU cc_start: 0.5829 (OUTLIER) cc_final: 0.5546 (mm) REVERT: A 767 GLN cc_start: 0.7350 (tt0) cc_final: 0.6440 (tm-30) REVERT: B 79 ARG cc_start: 0.7751 (ppt170) cc_final: 0.6695 (ppt170) REVERT: B 97 ILE cc_start: 0.8598 (pt) cc_final: 0.8330 (mt) REVERT: B 126 GLN cc_start: 0.6047 (tm-30) cc_final: 0.5664 (tt0) REVERT: B 130 ASP cc_start: 0.6725 (OUTLIER) cc_final: 0.6232 (p0) REVERT: B 239 MET cc_start: 0.4234 (mpp) cc_final: 0.2890 (mtt) REVERT: B 313 MET cc_start: 0.5741 (tmm) cc_final: 0.5371 (tmm) REVERT: B 676 GLU cc_start: 0.7289 (tp30) cc_final: 0.6834 (mp0) REVERT: B 701 LYS cc_start: 0.7477 (mtpt) cc_final: 0.6627 (mttp) REVERT: C 25 LEU cc_start: 0.8202 (mp) cc_final: 0.7795 (tp) REVERT: E 788 GLN cc_start: 0.7588 (tp40) cc_final: 0.7233 (mm-40) REVERT: F 101 ASN cc_start: 0.8092 (t0) cc_final: 0.7739 (t0) REVERT: F 216 GLN cc_start: 0.6625 (OUTLIER) cc_final: 0.5525 (tt0) outliers start: 46 outliers final: 31 residues processed: 208 average time/residue: 0.1112 time to fit residues: 35.4903 Evaluate side-chains 197 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 159 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 948 GLU Chi-restraints excluded: chain A residue 953 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 978 THR Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 671 THR Chi-restraints excluded: chain C residue 9 ASP Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain E residue 662 VAL Chi-restraints excluded: chain E residue 746 ILE Chi-restraints excluded: chain E residue 774 ILE Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 216 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 114 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 138 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 56 ASN C 59 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.154464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.117923 restraints weight = 17962.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.116619 restraints weight = 15912.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.118562 restraints weight = 15135.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.119254 restraints weight = 10345.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.119773 restraints weight = 9860.358| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14202 Z= 0.141 Angle : 0.628 11.446 19333 Z= 0.302 Chirality : 0.048 0.344 2176 Planarity : 0.004 0.052 2361 Dihedral : 11.121 177.096 2178 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.02 % Allowed : 16.61 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.21), residues: 1599 helix: 1.49 (0.20), residues: 670 sheet: 0.08 (0.50), residues: 114 loop : -1.56 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 72 TYR 0.025 0.001 TYR E 649 PHE 0.018 0.001 PHE C 13 TRP 0.023 0.002 TRP A 973 HIS 0.003 0.001 HIS A 802 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (14198) covalent geometry : angle 0.62724 / 0.30 (19330) hydrogen bonds : bond 0.03667 / 2.40 ( 568) hydrogen bonds : angle 4.11985 / 2.94 ( 1605) metal coordination : bond 0.00338 / 0.17 ( 4) metal coordination : angle 1.82422 / 0.99 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 162 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8446 (pp) REVERT: A 181 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7753 (mm-30) REVERT: A 212 MET cc_start: 0.7357 (mtp) cc_final: 0.7084 (ttm) REVERT: A 254 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.7703 (pp) REVERT: A 306 VAL cc_start: 0.8502 (OUTLIER) cc_final: 0.8289 (p) REVERT: A 679 LYS cc_start: 0.7707 (tttt) cc_final: 0.7261 (tttm) REVERT: A 693 LEU cc_start: 0.5787 (OUTLIER) cc_final: 0.5510 (mm) REVERT: A 767 GLN cc_start: 0.7339 (tt0) cc_final: 0.6412 (tm-30) REVERT: B 79 ARG cc_start: 0.7707 (ppt170) cc_final: 0.6763 (ppt170) REVERT: B 97 ILE cc_start: 0.8657 (pt) cc_final: 0.8333 (mt) REVERT: B 126 GLN cc_start: 0.6094 (tm-30) cc_final: 0.5723 (tt0) REVERT: B 130 ASP cc_start: 0.6571 (OUTLIER) cc_final: 0.6095 (p0) REVERT: B 239 MET cc_start: 0.4227 (mpp) cc_final: 0.2903 (mtm) REVERT: B 313 MET cc_start: 0.5715 (tmm) cc_final: 0.5304 (tmm) REVERT: B 676 GLU cc_start: 0.7330 (tp30) cc_final: 0.6796 (mp0) REVERT: B 701 LYS cc_start: 0.7463 (mtpt) cc_final: 0.6630 (mttp) REVERT: C 25 LEU cc_start: 0.8254 (mp) cc_final: 0.7814 (tp) REVERT: E 788 GLN cc_start: 0.7605 (tp40) cc_final: 0.7232 (mm-40) REVERT: F 101 ASN cc_start: 0.8082 (t0) cc_final: 0.7741 (t0) REVERT: F 216 GLN cc_start: 0.6649 (OUTLIER) cc_final: 0.5532 (tt0) outliers start: 44 outliers final: 33 residues processed: 201 average time/residue: 0.1073 time to fit residues: 33.1360 Evaluate side-chains 202 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 162 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 948 GLU Chi-restraints excluded: chain A residue 953 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 978 THR Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 671 THR Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain E residue 662 VAL Chi-restraints excluded: chain E residue 746 ILE Chi-restraints excluded: chain E residue 774 ILE Chi-restraints excluded: chain E residue 780 ILE Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 216 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 102 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 145 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 119 optimal weight: 5.9990 chunk 113 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 65 optimal weight: 0.0370 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 56 ASN C 59 HIS ** F 185 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 = 0.4024 r_free = 0.4024 target = 0.157783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.121706 restraints weight = 17755.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.120915 restraints weight = 16132.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.122718 restraints weight = 14954.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.123545 restraints weight = 9949.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.124099 restraints weight = 9134.967| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14202 Z= 0.121 Angle : 0.620 12.597 19333 Z= 0.297 Chirality : 0.047 0.312 2176 Planarity : 0.004 0.051 2361 Dihedral : 11.036 176.155 2178 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.81 % Allowed : 16.95 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.21), residues: 1599 helix: 1.48 (0.20), residues: 673 sheet: 0.09 (0.49), residues: 114 loop : -1.54 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 72 TYR 0.025 0.001 TYR E 649 PHE 0.016 0.001 PHE C 84 TRP 0.028 0.002 TRP A 511 HIS 0.002 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (14198) covalent geometry : angle 0.61913 / 0.30 (19330) hydrogen bonds : bond 0.03456 / 2.27 ( 568) hydrogen bonds : angle 4.08837 / 2.90 ( 1605) metal coordination : bond 0.00425 / 0.21 ( 4) metal coordination : angle 2.05139 / 1.11 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3198 Ramachandran restraints generated. 1599 Oldfield, 0 Emsley, 1599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 167 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8457 (pp) REVERT: A 181 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7754 (mm-30) REVERT: A 212 MET cc_start: 0.7296 (mtp) cc_final: 0.6992 (ttm) REVERT: A 254 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.7690 (pp) REVERT: A 306 VAL cc_start: 0.8467 (OUTLIER) cc_final: 0.8262 (p) REVERT: A 624 VAL cc_start: 0.8669 (t) cc_final: 0.8457 (m) REVERT: A 679 LYS cc_start: 0.7671 (tttt) cc_final: 0.7303 (tttm) REVERT: A 693 LEU cc_start: 0.5880 (OUTLIER) cc_final: 0.5649 (mm) REVERT: A 767 GLN cc_start: 0.7307 (tt0) cc_final: 0.6426 (tm-30) REVERT: B 79 ARG cc_start: 0.7709 (ppt170) cc_final: 0.6792 (ppt170) REVERT: B 97 ILE cc_start: 0.8634 (pt) cc_final: 0.8271 (mt) REVERT: B 126 GLN cc_start: 0.6041 (tm-30) cc_final: 0.5694 (tt0) REVERT: B 130 ASP cc_start: 0.6548 (OUTLIER) cc_final: 0.6079 (p0) REVERT: B 239 MET cc_start: 0.3877 (mpp) cc_final: 0.2499 (mtm) REVERT: B 313 MET cc_start: 0.5714 (tmm) cc_final: 0.5329 (tmm) REVERT: B 676 GLU cc_start: 0.7288 (tp30) cc_final: 0.6844 (mp0) REVERT: B 701 LYS cc_start: 0.7690 (mtpt) cc_final: 0.6829 (mttp) REVERT: C 25 LEU cc_start: 0.8138 (mp) cc_final: 0.7738 (tp) REVERT: E 757 GLN cc_start: 0.7514 (OUTLIER) cc_final: 0.7141 (mm110) REVERT: E 788 GLN cc_start: 0.7569 (tp40) cc_final: 0.7223 (mm-40) REVERT: F 101 ASN cc_start: 0.8051 (t0) cc_final: 0.7706 (t0) REVERT: F 216 GLN cc_start: 0.6610 (OUTLIER) cc_final: 0.5481 (tt0) outliers start: 41 outliers final: 31 residues processed: 203 average time/residue: 0.1049 time to fit residues: 32.5912 Evaluate side-chains 199 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 160 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 530 ASP Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 812 ASP Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 948 GLU Chi-restraints excluded: chain A residue 953 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 978 THR Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 671 THR Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain E residue 662 VAL Chi-restraints excluded: chain E residue 746 ILE Chi-restraints excluded: chain E residue 757 GLN Chi-restraints excluded: chain E residue 774 ILE Chi-restraints excluded: chain E residue 780 ILE Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 216 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 5 optimal weight: 1.9990 chunk 160 optimal weight: 0.5980 chunk 47 optimal weight: 0.2980 chunk 65 optimal weight: 0.0970 chunk 25 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 105 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 193 GLN C 56 ASN C 59 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.157475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.121523 restraints weight = 17691.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.120624 restraints weight = 15434.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.122457 restraints weight = 16078.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.123590 restraints weight = 10186.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.124385 restraints weight = 9041.366| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14202 Z= 0.126 Angle : 0.621 12.037 19333 Z= 0.300 Chirality : 0.047 0.287 2176 Planarity : 0.004 0.050 2361 Dihedral : 10.985 175.150 2178 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.09 % Allowed : 16.61 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.21), residues: 1599 helix: 1.52 (0.20), residues: 671 sheet: 0.09 (0.49), residues: 114 loop : -1.54 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 72 TYR 0.022 0.001 TYR E 649 PHE 0.015 0.001 PHE C 84 TRP 0.022 0.002 TRP A 973 HIS 0.002 0.001 HIS E 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (14198) covalent geometry : angle 0.62089 / 0.30 (19330) hydrogen bonds : bond 0.03498 / 2.30 ( 568) hydrogen bonds : angle 4.08330 / 2.89 ( 1605) metal coordination : bond 0.00377 / 0.19 ( 4) metal coordination : angle 1.57815 / 0.87 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3394.94 seconds wall clock time: 58 minutes 56.45 seconds (3536.45 seconds total)