Starting phenix.real_space_refine on Fri Mar 14 06:54:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xjz_33238/03_2025/7xjz_33238.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xjz_33238/03_2025/7xjz_33238.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xjz_33238/03_2025/7xjz_33238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xjz_33238/03_2025/7xjz_33238.map" model { file = "/net/cci-nas-00/data/ceres_data/7xjz_33238/03_2025/7xjz_33238.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xjz_33238/03_2025/7xjz_33238.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.073 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 75 5.49 5 S 31 5.16 5 C 5618 2.51 5 N 1594 2.21 5 O 1958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9276 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7716 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 983, 7711 Classifications: {'peptide': 983} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 3, 'PTRANS': 43, 'TRANS': 936} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 58 Conformer: "B" Number of residues, atoms: 983, 7711 Classifications: {'peptide': 983} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 3, 'PTRANS': 43, 'TRANS': 936} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 58 bond proxies already assigned to first conformer: 7862 Chain: "B" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1560 Unusual residues: {'GTP': 1} Classifications: {'RNA': 72, 'undetermined': 1} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 31, 'rna3p_pyr': 33} Link IDs: {'rna2p': 8, 'rna3p': 63, None: 1} Not linked: pdbres="GTP B 1 " pdbres=" C B 2 " Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AALA A 940 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA A 940 " occ=0.50 Time building chain proxies: 9.33, per 1000 atoms: 1.01 Number of scatterers: 9276 At special positions: 0 Unit cell: (123.2, 107.8, 106.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 31 16.00 P 75 15.00 O 1958 8.00 N 1594 7.00 C 5618 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 2.0 seconds 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1848 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 8 sheets defined 52.0% alpha, 13.1% beta 16 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 3.63 Creating SS restraints... Processing helix chain 'A' and resid 73 through 89 removed outlier: 3.814A pdb=" N ILE A 78 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLN A 79 " --> pdb=" O GLN A 75 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP A 83 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N TRP A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY A 89 " --> pdb=" O TRP A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 133 Processing helix chain 'A' and resid 158 through 171 removed outlier: 3.997A pdb=" N PHE A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU A 164 " --> pdb=" O GLN A 160 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 240 removed outlier: 4.122A pdb=" N LEU A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 274 removed outlier: 3.985A pdb=" N GLU A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N MET A 267 " --> pdb=" O ASN A 263 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N HIS A 274 " --> pdb=" O TYR A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 296 removed outlier: 4.111A pdb=" N ILE A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN A 281 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS A 282 " --> pdb=" O ASP A 278 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASP A 285 " --> pdb=" O GLN A 281 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP A 286 " --> pdb=" O LYS A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 321 removed outlier: 3.501A pdb=" N ALA A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 308 " --> pdb=" O TYR A 304 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS A 309 " --> pdb=" O ASP A 305 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 352 removed outlier: 4.153A pdb=" N ARG A 330 " --> pdb=" O THR A 326 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TRP A 346 " --> pdb=" O CYS A 342 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL A 347 " --> pdb=" O ALA A 343 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS A 348 " --> pdb=" O GLN A 344 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASN A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 418 removed outlier: 3.538A pdb=" N LYS A 405 " --> pdb=" O ILE A 401 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 410 " --> pdb=" O GLN A 406 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN A 413 " --> pdb=" O LYS A 409 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE A 414 " --> pdb=" O SER A 410 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLU A 416 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 461 Processing helix chain 'A' and resid 468 through 479 removed outlier: 3.636A pdb=" N GLU A 472 " --> pdb=" O THR A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 485 Processing helix chain 'A' and resid 508 through 521 Proline residue: A 516 - end of helix removed outlier: 3.643A pdb=" N SER A 520 " --> pdb=" O PRO A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 591 removed outlier: 3.572A pdb=" N GLU A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 613 removed outlier: 3.875A pdb=" N HIS A 606 " --> pdb=" O GLN A 602 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP A 607 " --> pdb=" O ARG A 603 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER A 609 " --> pdb=" O LEU A 605 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE A 610 " --> pdb=" O HIS A 606 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU A 613 " --> pdb=" O SER A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 631 removed outlier: 4.119A pdb=" N GLU A 628 " --> pdb=" O SER A 624 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN A 631 " --> pdb=" O GLN A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 650 removed outlier: 3.835A pdb=" N PHE A 647 " --> pdb=" O ASP A 644 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA A 649 " --> pdb=" O SER A 646 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU A 650 " --> pdb=" O PHE A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 662 removed outlier: 3.684A pdb=" N LEU A 655 " --> pdb=" O PRO A 651 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 656 " --> pdb=" O LYS A 652 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR A 657 " --> pdb=" O ASP A 653 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N HIS A 662 " --> pdb=" O VAL A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 716 removed outlier: 3.764A pdb=" N VAL A 693 " --> pdb=" O LYS A 689 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG A 694 " --> pdb=" O GLU A 690 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA A 699 " --> pdb=" O LYS A 695 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL A 700 " --> pdb=" O GLY A 696 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA A 703 " --> pdb=" O ALA A 699 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR A 705 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU A 706 " --> pdb=" O ARG A 702 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP A 707 " --> pdb=" O ALA A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 729 removed outlier: 4.403A pdb=" N LEU A 727 " --> pdb=" O ARG A 724 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER A 728 " --> pdb=" O ASP A 725 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N SER A 729 " --> pdb=" O GLN A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 757 removed outlier: 5.065A pdb=" N ALA A 751 " --> pdb=" O GLU A 747 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N GLU A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL A 753 " --> pdb=" O THR A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 762 No H-bonds generated for 'chain 'A' and resid 760 through 762' Processing helix chain 'A' and resid 763 through 771 removed outlier: 3.663A pdb=" N ILE A 767 " --> pdb=" O MET A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 780 removed outlier: 3.709A pdb=" N ALA A 779 " --> pdb=" O SER A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 786 removed outlier: 4.254A pdb=" N GLU A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE A 786 " --> pdb=" O ILE A 782 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 781 through 786' Processing helix chain 'A' and resid 787 through 790 Processing helix chain 'A' and resid 792 through 802 removed outlier: 3.517A pdb=" N GLY A 802 " --> pdb=" O ALA A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 813 removed outlier: 3.735A pdb=" N ALA A 808 " --> pdb=" O SER A 804 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU A 809 " --> pdb=" O GLU A 805 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA A 810 " --> pdb=" O GLN A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 848 removed outlier: 3.620A pdb=" N VAL A 832 " --> pdb=" O ASP A 828 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 833 " --> pdb=" O PRO A 829 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA A 848 " --> pdb=" O GLY A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 874 Processing helix chain 'A' and resid 880 through 891 removed outlier: 4.097A pdb=" N THR A 886 " --> pdb=" O THR A 882 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 887 " --> pdb=" O LYS A 883 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU A 891 " --> pdb=" O LEU A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 917 removed outlier: 4.424A pdb=" N ILE A 901 " --> pdb=" O ASP A 897 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP A 902 " --> pdb=" O SER A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 930 removed outlier: 3.580A pdb=" N SER A 928 " --> pdb=" O GLU A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 951 removed outlier: 4.004A pdb=" N GLU A 946 " --> pdb=" O GLN A 942 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU A 948 " --> pdb=" O ALA A 944 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA A 949 " --> pdb=" O ILE A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 964 removed outlier: 3.754A pdb=" N SER A 964 " --> pdb=" O VAL A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 971 removed outlier: 3.545A pdb=" N ILE A 970 " --> pdb=" O PRO A 966 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG A 971 " --> pdb=" O THR A 967 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 966 through 971' Processing helix chain 'A' and resid 974 through 978 Processing helix chain 'A' and resid 988 through 1003 removed outlier: 3.906A pdb=" N ARG A 992 " --> pdb=" O LYS A 988 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP A1003 " --> pdb=" O LEU A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1019 Processing helix chain 'A' and resid 1021 through 1032 removed outlier: 3.804A pdb=" N LEU A1025 " --> pdb=" O LEU A1021 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU A1026 " --> pdb=" O LEU A1022 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP A1027 " --> pdb=" O GLN A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1054 Processing sheet with id=AA1, first strand: chain 'A' and resid 91 through 92 removed outlier: 3.802A pdb=" N ALA A 122 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE A 207 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLU A 206 " --> pdb=" O MET A 202 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N MET A 202 " --> pdb=" O GLU A 206 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR A 208 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP A 194 " --> pdb=" O GLN A 214 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 179 through 183 removed outlier: 6.582A pdb=" N TRP A 194 " --> pdb=" O GLN A 214 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR A 208 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N MET A 202 " --> pdb=" O GLU A 206 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLU A 206 " --> pdb=" O MET A 202 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 425 through 430 removed outlier: 3.775A pdb=" N LEU A 434 " --> pdb=" O ILE A 390 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE A 390 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASN A 440 " --> pdb=" O ARG A 384 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ARG A 384 " --> pdb=" O ASN A 440 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 450 through 451 Processing sheet with id=AA5, first strand: chain 'A' and resid 555 through 556 Processing sheet with id=AA6, first strand: chain 'A' and resid 564 through 565 Processing sheet with id=AA7, first strand: chain 'A' and resid 617 through 619 removed outlier: 7.056A pdb=" N PHE A 666 " --> pdb=" O CYS A 679 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N CYS A 679 " --> pdb=" O PHE A 666 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VAL A 668 " --> pdb=" O LEU A 677 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N MET A 637 " --> pdb=" O ALA A 684 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 731 through 733 removed outlier: 6.322A pdb=" N GLY A 737 " --> pdb=" O PHE A 732 " (cutoff:3.500A) 331 hydrogen bonds defined for protein. 925 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 44 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 4.27 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1408 1.31 - 1.44: 2901 1.44 - 1.56: 5105 1.56 - 1.68: 148 1.68 - 1.81: 52 Bond restraints: 9614 Sorted by residual: bond pdb=" C2 GTP B 1 " pdb=" N2 GTP B 1 " ideal model delta sigma weight residual 1.330 1.454 -0.124 2.00e-02 2.50e+03 3.84e+01 bond pdb=" N THR A 967 " pdb=" CA THR A 967 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.21e-02 6.83e+03 1.03e+01 bond pdb=" N ARG A 965 " pdb=" CA ARG A 965 " ideal model delta sigma weight residual 1.461 1.488 -0.027 9.20e-03 1.18e+04 8.71e+00 bond pdb=" N ASN A 697 " pdb=" CA ASN A 697 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.18e+00 bond pdb=" N ILE A 945 " pdb=" CA ILE A 945 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.33e-02 5.65e+03 8.00e+00 ... (remaining 9609 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 13156 1.83 - 3.66: 191 3.66 - 5.49: 30 5.49 - 7.32: 8 7.32 - 9.15: 6 Bond angle restraints: 13391 Sorted by residual: angle pdb=" N ARG A 965 " pdb=" CA ARG A 965 " pdb=" C ARG A 965 " ideal model delta sigma weight residual 112.75 103.96 8.79 1.36e+00 5.41e-01 4.18e+01 angle pdb=" C PRO A 966 " pdb=" CA PRO A 966 " pdb=" CB PRO A 966 " ideal model delta sigma weight residual 112.64 105.72 6.92 1.74e+00 3.30e-01 1.58e+01 angle pdb=" CA ALA A 962 " pdb=" C ALA A 962 " pdb=" O ALA A 962 " ideal model delta sigma weight residual 120.90 117.03 3.87 1.03e+00 9.43e-01 1.41e+01 angle pdb=" CA GLY A1067 " pdb=" C GLY A1067 " pdb=" O GLY A1067 " ideal model delta sigma weight residual 120.80 117.50 3.30 9.80e-01 1.04e+00 1.13e+01 angle pdb=" CA THR A 967 " pdb=" C THR A 967 " pdb=" O THR A 967 " ideal model delta sigma weight residual 120.55 117.06 3.49 1.06e+00 8.90e-01 1.08e+01 ... (remaining 13386 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.00: 5582 30.00 - 60.00: 244 60.00 - 90.00: 66 90.00 - 120.00: 2 120.00 - 150.00: 1 Dihedral angle restraints: 5895 sinusoidal: 3037 harmonic: 2858 Sorted by residual: dihedral pdb=" O4' U B 19 " pdb=" C1' U B 19 " pdb=" N1 U B 19 " pdb=" C2 U B 19 " ideal model delta sinusoidal sigma weight residual 200.00 50.00 150.00 1 1.50e+01 4.44e-03 7.96e+01 dihedral pdb=" C8 GTP B 1 " pdb=" C1' GTP B 1 " pdb=" N9 GTP B 1 " pdb=" O4' GTP B 1 " ideal model delta sinusoidal sigma weight residual 104.59 6.23 98.37 1 2.00e+01 2.50e-03 2.75e+01 dihedral pdb=" O2G GTP B 1 " pdb=" O3B GTP B 1 " pdb=" PG GTP B 1 " pdb=" PB GTP B 1 " ideal model delta sinusoidal sigma weight residual 177.30 -86.23 -96.47 1 2.00e+01 2.50e-03 2.67e+01 ... (remaining 5892 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1220 0.043 - 0.087: 274 0.087 - 0.130: 72 0.130 - 0.174: 8 0.174 - 0.217: 3 Chirality restraints: 1577 Sorted by residual: chirality pdb=" CA SER A 964 " pdb=" N SER A 964 " pdb=" C SER A 964 " pdb=" CB SER A 964 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" C2' C B 2 " pdb=" C3' C B 2 " pdb=" O2' C B 2 " pdb=" C1' C B 2 " both_signs ideal model delta sigma weight residual False -2.75 -2.58 -0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" C3' GTP B 1 " pdb=" C2' GTP B 1 " pdb=" C4' GTP B 1 " pdb=" O3' GTP B 1 " both_signs ideal model delta sigma weight residual False -2.47 -2.65 0.17 2.00e-01 2.50e+01 7.56e-01 ... (remaining 1574 not shown) Planarity restraints: 1461 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 637 " -0.028 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO A 638 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 638 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 638 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A1063 " 0.008 2.00e-02 2.50e+03 1.56e-02 2.42e+00 pdb=" C SER A1063 " -0.027 2.00e-02 2.50e+03 pdb=" O SER A1063 " 0.010 2.00e-02 2.50e+03 pdb=" N VAL A1064 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 969 " 0.007 2.00e-02 2.50e+03 1.51e-02 2.29e+00 pdb=" C ILE A 969 " -0.026 2.00e-02 2.50e+03 pdb=" O ILE A 969 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE A 970 " 0.009 2.00e-02 2.50e+03 ... (remaining 1458 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1359 2.75 - 3.29: 8903 3.29 - 3.83: 15407 3.83 - 4.36: 17335 4.36 - 4.90: 28389 Nonbonded interactions: 71393 Sorted by model distance: nonbonded pdb=" O PHE A 950 " pdb=" OG1 THR A 953 " model vdw 2.218 3.040 nonbonded pdb=" OG1 THR A 855 " pdb=" OP1 G B 69 " model vdw 2.220 3.040 nonbonded pdb=" O GLU A 206 " pdb=" NH1 ARG A 234 " model vdw 2.241 3.120 nonbonded pdb=" OE1 GLU A 389 " pdb=" OH TYR A 584 " model vdw 2.244 3.040 nonbonded pdb=" OG1 THR A 255 " pdb=" OE1 GLU A 258 " model vdw 2.248 3.040 ... (remaining 71388 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=0.50 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 32.920 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 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 : 0.004 0.124 9614 Z= 0.229 Angle : 0.591 9.148 13391 Z= 0.321 Chirality : 0.040 0.217 1577 Planarity : 0.004 0.043 1461 Dihedral : 16.502 149.999 4047 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.13 % Allowed : 8.19 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.27), residues: 982 helix: -0.15 (0.26), residues: 439 sheet: -0.34 (0.52), residues: 119 loop : -1.59 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 194 HIS 0.004 0.001 HIS A 145 PHE 0.010 0.001 PHE A 544 TYR 0.012 0.001 TYR A 230 ARG 0.002 0.000 ARG A1045 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 1.439 Fit side-chains revert: symmetry clash REVERT: A 263 ASN cc_start: 0.7814 (t0) cc_final: 0.7556 (t0) REVERT: A 267 MET cc_start: 0.9033 (mmm) cc_final: 0.8695 (mmp) REVERT: A 495 TYR cc_start: 0.4079 (OUTLIER) cc_final: 0.2605 (m-80) REVERT: A 597 MET cc_start: 0.8677 (tmm) cc_final: 0.8469 (tmm) REVERT: A 653 ASP cc_start: 0.8157 (p0) cc_final: 0.7514 (t0) REVERT: A 714 MET cc_start: 0.8508 (tmm) cc_final: 0.8173 (tmm) REVERT: A 775 MET cc_start: 0.8274 (tmm) cc_final: 0.7898 (tmm) REVERT: A 793 MET cc_start: 0.8824 (mmm) cc_final: 0.8494 (mmm) REVERT: A 875 ASN cc_start: 0.8994 (OUTLIER) cc_final: 0.8726 (m-40) REVERT: A 963 TYR cc_start: 0.8811 (OUTLIER) cc_final: 0.7770 (t80) outliers start: 26 outliers final: 7 residues processed: 113 average time/residue: 0.2802 time to fit residues: 42.2698 Evaluate side-chains 62 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 963 TYR Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 1064 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 44 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 31 optimal weight: 0.0050 chunk 50 optimal weight: 0.0070 chunk 61 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 overall best weight: 1.1616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 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 = 0.3656 r_free = 0.3656 target = 0.097539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.075514 restraints weight = 26272.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.077069 restraints weight = 13856.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.077656 restraints weight = 9866.885| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3230 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9614 Z= 0.177 Angle : 0.557 8.311 13391 Z= 0.283 Chirality : 0.040 0.157 1577 Planarity : 0.004 0.043 1461 Dihedral : 17.768 149.599 2215 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.77 % Allowed : 12.17 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.27), residues: 982 helix: 0.13 (0.26), residues: 448 sheet: -0.08 (0.54), residues: 110 loop : -1.65 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 542 HIS 0.004 0.001 HIS A 145 PHE 0.024 0.001 PHE A 260 TYR 0.014 0.001 TYR A 230 ARG 0.005 0.001 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 59 time to evaluate : 0.773 Fit side-chains revert: symmetry clash REVERT: A 93 MET cc_start: 0.7897 (mtm) cc_final: 0.7671 (mtp) REVERT: A 237 MET cc_start: 0.8269 (ttt) cc_final: 0.7947 (ttt) REVERT: A 263 ASN cc_start: 0.7923 (t0) cc_final: 0.7590 (t0) REVERT: A 267 MET cc_start: 0.9008 (mmm) cc_final: 0.8738 (mmp) REVERT: A 495 TYR cc_start: 0.4436 (OUTLIER) cc_final: 0.2791 (m-80) REVERT: A 597 MET cc_start: 0.8664 (tmm) cc_final: 0.8450 (tmm) REVERT: A 653 ASP cc_start: 0.7831 (p0) cc_final: 0.7580 (t0) REVERT: A 714 MET cc_start: 0.8417 (tmm) cc_final: 0.8108 (tmm) REVERT: A 726 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7692 (pp30) REVERT: A 775 MET cc_start: 0.8122 (tmm) cc_final: 0.7921 (tmm) REVERT: A 793 MET cc_start: 0.8815 (mmm) cc_final: 0.8501 (mmm) REVERT: A 875 ASN cc_start: 0.9063 (OUTLIER) cc_final: 0.8801 (m-40) REVERT: A 906 GLN cc_start: 0.8053 (tm-30) cc_final: 0.7850 (tm-30) REVERT: A 963 TYR cc_start: 0.8798 (OUTLIER) cc_final: 0.8113 (t80) outliers start: 23 outliers final: 9 residues processed: 77 average time/residue: 0.1833 time to fit residues: 20.9960 Evaluate side-chains 67 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 726 GLN Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 963 TYR Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 1064 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 18 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 33 optimal weight: 0.0010 chunk 52 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 89 optimal weight: 20.0000 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 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 = 0.3667 r_free = 0.3667 target = 0.098224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.075688 restraints weight = 26666.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.077544 restraints weight = 14541.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.078779 restraints weight = 9425.981| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3264 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3264 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9614 Z= 0.139 Angle : 0.520 7.069 13391 Z= 0.260 Chirality : 0.039 0.173 1577 Planarity : 0.004 0.043 1461 Dihedral : 17.508 149.724 2211 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.53 % Allowed : 12.89 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.27), residues: 982 helix: 0.30 (0.26), residues: 445 sheet: -0.18 (0.53), residues: 110 loop : -1.60 (0.27), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 542 HIS 0.004 0.001 HIS A 274 PHE 0.007 0.001 PHE A 950 TYR 0.011 0.001 TYR A 230 ARG 0.006 0.000 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 ASN cc_start: 0.7905 (t0) cc_final: 0.7636 (t0) REVERT: A 267 MET cc_start: 0.9013 (mmm) cc_final: 0.8798 (mmp) REVERT: A 495 TYR cc_start: 0.4046 (OUTLIER) cc_final: 0.2556 (m-80) REVERT: A 597 MET cc_start: 0.8667 (tmm) cc_final: 0.8421 (tmm) REVERT: A 653 ASP cc_start: 0.7843 (p0) cc_final: 0.7616 (t0) REVERT: A 793 MET cc_start: 0.8796 (mmm) cc_final: 0.8498 (mmm) REVERT: A 875 ASN cc_start: 0.9071 (OUTLIER) cc_final: 0.8825 (m-40) REVERT: A 906 GLN cc_start: 0.7924 (tm-30) cc_final: 0.7535 (tm-30) REVERT: A 963 TYR cc_start: 0.8780 (OUTLIER) cc_final: 0.8001 (t80) REVERT: A 1052 VAL cc_start: 0.8181 (t) cc_final: 0.7967 (t) outliers start: 21 outliers final: 10 residues processed: 74 average time/residue: 0.2052 time to fit residues: 22.0064 Evaluate side-chains 65 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 910 ARG Chi-restraints excluded: chain A residue 963 TYR Chi-restraints excluded: chain A residue 1064 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 89 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 GLN ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.095478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.073630 restraints weight = 26558.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.074792 restraints weight = 13911.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.075475 restraints weight = 10182.997| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9614 Z= 0.233 Angle : 0.581 15.786 13391 Z= 0.289 Chirality : 0.041 0.159 1577 Planarity : 0.004 0.051 1461 Dihedral : 17.572 148.339 2210 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.53 % Allowed : 13.13 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.27), residues: 982 helix: 0.28 (0.26), residues: 443 sheet: -0.14 (0.53), residues: 111 loop : -1.64 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 198 HIS 0.003 0.001 HIS A 312 PHE 0.020 0.001 PHE A 986 TYR 0.020 0.001 TYR A 230 ARG 0.003 0.000 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 51 time to evaluate : 0.997 Fit side-chains REVERT: A 237 MET cc_start: 0.8283 (ttt) cc_final: 0.7979 (ttt) REVERT: A 263 ASN cc_start: 0.7924 (t0) cc_final: 0.7655 (t0) REVERT: A 278 ASP cc_start: 0.7393 (p0) cc_final: 0.7088 (p0) REVERT: A 495 TYR cc_start: 0.4542 (OUTLIER) cc_final: 0.2814 (m-80) REVERT: A 597 MET cc_start: 0.8713 (tmm) cc_final: 0.8502 (tmm) REVERT: A 726 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7840 (tm-30) REVERT: A 743 MET cc_start: 0.8778 (mmt) cc_final: 0.8133 (mmm) REVERT: A 775 MET cc_start: 0.7891 (tmm) cc_final: 0.7075 (tmm) REVERT: A 793 MET cc_start: 0.8877 (mmm) cc_final: 0.8503 (mmm) REVERT: A 875 ASN cc_start: 0.9047 (OUTLIER) cc_final: 0.8806 (m-40) REVERT: A 963 TYR cc_start: 0.8893 (OUTLIER) cc_final: 0.7968 (t80) outliers start: 21 outliers final: 13 residues processed: 66 average time/residue: 0.2087 time to fit residues: 20.4558 Evaluate side-chains 67 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 330 ARG Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 726 GLN Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 963 TYR Chi-restraints excluded: chain A residue 1064 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 57 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 80 optimal weight: 0.0370 overall best weight: 1.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 906 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 = 0.3642 r_free = 0.3642 target = 0.096638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.074690 restraints weight = 26481.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.076289 restraints weight = 13777.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.076843 restraints weight = 9901.400| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3221 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9614 Z= 0.162 Angle : 0.536 13.065 13391 Z= 0.264 Chirality : 0.039 0.169 1577 Planarity : 0.004 0.047 1461 Dihedral : 17.477 148.105 2210 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.41 % Allowed : 13.37 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.27), residues: 982 helix: 0.37 (0.26), residues: 446 sheet: -0.11 (0.54), residues: 111 loop : -1.52 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 542 HIS 0.003 0.001 HIS A 145 PHE 0.009 0.001 PHE A 986 TYR 0.014 0.001 TYR A 230 ARG 0.004 0.000 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 1.013 Fit side-chains REVERT: A 160 GLN cc_start: 0.8567 (pt0) cc_final: 0.8316 (pt0) REVERT: A 263 ASN cc_start: 0.7828 (t0) cc_final: 0.7600 (t0) REVERT: A 495 TYR cc_start: 0.4594 (OUTLIER) cc_final: 0.2854 (m-80) REVERT: A 597 MET cc_start: 0.8747 (tmm) cc_final: 0.8501 (tmm) REVERT: A 726 GLN cc_start: 0.8041 (pp30) cc_final: 0.7712 (tm-30) REVERT: A 793 MET cc_start: 0.8749 (mmm) cc_final: 0.8529 (mmm) REVERT: A 875 ASN cc_start: 0.9053 (OUTLIER) cc_final: 0.8838 (m-40) REVERT: A 963 TYR cc_start: 0.8881 (OUTLIER) cc_final: 0.7939 (t80) outliers start: 20 outliers final: 12 residues processed: 69 average time/residue: 0.2091 time to fit residues: 21.4241 Evaluate side-chains 65 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 963 TYR Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1064 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 42 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 48 optimal weight: 9.9990 chunk 75 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 99 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.096640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.073431 restraints weight = 26667.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.075362 restraints weight = 14291.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.076648 restraints weight = 9228.947| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9614 Z= 0.143 Angle : 0.526 12.997 13391 Z= 0.258 Chirality : 0.038 0.162 1577 Planarity : 0.004 0.044 1461 Dihedral : 17.403 148.569 2210 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.29 % Allowed : 13.86 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.27), residues: 982 helix: 0.45 (0.26), residues: 448 sheet: -0.04 (0.53), residues: 111 loop : -1.44 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 542 HIS 0.002 0.000 HIS A 145 PHE 0.009 0.001 PHE A 950 TYR 0.013 0.001 TYR A 230 ARG 0.003 0.000 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 52 time to evaluate : 0.901 Fit side-chains REVERT: A 160 GLN cc_start: 0.8560 (pt0) cc_final: 0.8190 (pt0) REVERT: A 278 ASP cc_start: 0.7409 (p0) cc_final: 0.7068 (p0) REVERT: A 495 TYR cc_start: 0.4552 (OUTLIER) cc_final: 0.2772 (m-80) REVERT: A 597 MET cc_start: 0.8749 (tmm) cc_final: 0.8507 (tmm) REVERT: A 726 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7809 (tm-30) REVERT: A 793 MET cc_start: 0.8762 (mmm) cc_final: 0.8539 (mmm) REVERT: A 875 ASN cc_start: 0.9091 (OUTLIER) cc_final: 0.8850 (m-40) REVERT: A 947 MET cc_start: 0.7947 (ttp) cc_final: 0.7583 (ttp) REVERT: A 963 TYR cc_start: 0.8955 (OUTLIER) cc_final: 0.7929 (t80) REVERT: A 1052 VAL cc_start: 0.8163 (t) cc_final: 0.7935 (t) outliers start: 19 outliers final: 10 residues processed: 65 average time/residue: 0.1841 time to fit residues: 18.0589 Evaluate side-chains 62 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 726 GLN Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 963 TYR Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1064 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 50 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 28 optimal weight: 0.1980 chunk 14 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 263 ASN A 341 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.097611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.074829 restraints weight = 26777.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.076669 restraints weight = 14729.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.077884 restraints weight = 9648.503| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3244 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3244 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9614 Z= 0.134 Angle : 0.525 13.932 13391 Z= 0.254 Chirality : 0.038 0.157 1577 Planarity : 0.004 0.042 1461 Dihedral : 17.304 149.039 2206 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.05 % Allowed : 14.70 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.27), residues: 982 helix: 0.59 (0.26), residues: 446 sheet: 0.02 (0.53), residues: 111 loop : -1.36 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 542 HIS 0.002 0.000 HIS A 145 PHE 0.007 0.001 PHE A 950 TYR 0.011 0.001 TYR A 230 ARG 0.003 0.000 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 0.914 Fit side-chains REVERT: A 160 GLN cc_start: 0.8514 (pt0) cc_final: 0.8173 (pt0) REVERT: A 495 TYR cc_start: 0.4339 (OUTLIER) cc_final: 0.2567 (m-80) REVERT: A 597 MET cc_start: 0.8730 (tmm) cc_final: 0.8477 (tmm) REVERT: A 726 GLN cc_start: 0.8031 (pp30) cc_final: 0.7812 (tm-30) REVERT: A 775 MET cc_start: 0.8502 (tmm) cc_final: 0.7980 (tmm) REVERT: A 963 TYR cc_start: 0.8950 (OUTLIER) cc_final: 0.7934 (t80) REVERT: A 1052 VAL cc_start: 0.8094 (t) cc_final: 0.7845 (t) outliers start: 17 outliers final: 11 residues processed: 64 average time/residue: 0.1891 time to fit residues: 18.3938 Evaluate side-chains 60 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 963 TYR Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1064 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 35 optimal weight: 0.6980 chunk 37 optimal weight: 8.9990 chunk 3 optimal weight: 0.0970 chunk 104 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.096409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.074767 restraints weight = 26621.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.076431 restraints weight = 14458.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.077037 restraints weight = 9013.972| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9614 Z= 0.171 Angle : 0.539 12.590 13391 Z= 0.263 Chirality : 0.039 0.154 1577 Planarity : 0.004 0.044 1461 Dihedral : 17.302 148.604 2204 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.81 % Allowed : 14.94 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.27), residues: 982 helix: 0.63 (0.26), residues: 447 sheet: -0.02 (0.53), residues: 111 loop : -1.39 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 542 HIS 0.003 0.001 HIS A 145 PHE 0.009 0.001 PHE A 950 TYR 0.015 0.001 TYR A 230 ARG 0.004 0.000 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.960 Fit side-chains REVERT: A 160 GLN cc_start: 0.8506 (pt0) cc_final: 0.8245 (pt0) REVERT: A 278 ASP cc_start: 0.7437 (p0) cc_final: 0.7067 (p0) REVERT: A 495 TYR cc_start: 0.4692 (OUTLIER) cc_final: 0.2815 (m-80) REVERT: A 597 MET cc_start: 0.8758 (tmm) cc_final: 0.8510 (tmm) REVERT: A 726 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7851 (tm-30) REVERT: A 775 MET cc_start: 0.8487 (tmm) cc_final: 0.8061 (tmm) REVERT: A 963 TYR cc_start: 0.8995 (OUTLIER) cc_final: 0.7934 (t80) outliers start: 15 outliers final: 11 residues processed: 57 average time/residue: 0.1975 time to fit residues: 17.3408 Evaluate side-chains 62 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 726 GLN Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 963 TYR Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1064 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 103 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 70 optimal weight: 0.2980 chunk 4 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.095629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.073816 restraints weight = 26300.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.075588 restraints weight = 14415.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.076220 restraints weight = 8719.185| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9614 Z= 0.199 Angle : 0.547 12.239 13391 Z= 0.268 Chirality : 0.039 0.152 1577 Planarity : 0.004 0.048 1461 Dihedral : 17.324 147.898 2204 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.05 % Allowed : 14.70 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.27), residues: 982 helix: 0.68 (0.26), residues: 449 sheet: -0.02 (0.54), residues: 111 loop : -1.36 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 542 HIS 0.003 0.001 HIS A 145 PHE 0.010 0.001 PHE A 950 TYR 0.017 0.001 TYR A 230 ARG 0.004 0.000 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 0.919 Fit side-chains REVERT: A 160 GLN cc_start: 0.8529 (pt0) cc_final: 0.8264 (pt0) REVERT: A 495 TYR cc_start: 0.4916 (OUTLIER) cc_final: 0.2968 (m-80) REVERT: A 597 MET cc_start: 0.8780 (tmm) cc_final: 0.8534 (tmm) REVERT: A 726 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7882 (tm-30) REVERT: A 947 MET cc_start: 0.7991 (ttp) cc_final: 0.7669 (ttp) REVERT: A 963 TYR cc_start: 0.9033 (OUTLIER) cc_final: 0.7923 (t80) outliers start: 17 outliers final: 12 residues processed: 58 average time/residue: 0.1921 time to fit residues: 17.0119 Evaluate side-chains 61 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 726 GLN Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 963 TYR Chi-restraints excluded: chain A residue 1064 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 2 optimal weight: 0.4980 chunk 85 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 83 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 14 optimal weight: 0.0040 chunk 0 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 overall best weight: 1.0796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.096370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.074726 restraints weight = 26469.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.075954 restraints weight = 14257.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.076470 restraints weight = 10818.847| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 9614 Z= 0.155 Angle : 0.562 20.993 13391 Z= 0.270 Chirality : 0.039 0.157 1577 Planarity : 0.004 0.045 1461 Dihedral : 17.301 147.821 2204 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.57 % Allowed : 15.42 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.27), residues: 982 helix: 0.68 (0.26), residues: 449 sheet: -0.02 (0.53), residues: 111 loop : -1.35 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 542 HIS 0.003 0.001 HIS A 145 PHE 0.009 0.001 PHE A 950 TYR 0.014 0.001 TYR A 230 ARG 0.004 0.000 ARG A 144 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 1.023 Fit side-chains REVERT: A 160 GLN cc_start: 0.8501 (pt0) cc_final: 0.8258 (pt0) REVERT: A 495 TYR cc_start: 0.4842 (OUTLIER) cc_final: 0.3013 (m-80) REVERT: A 597 MET cc_start: 0.8761 (tmm) cc_final: 0.8520 (tmm) REVERT: A 726 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7873 (tm-30) REVERT: A 947 MET cc_start: 0.7978 (ttp) cc_final: 0.7738 (ttp) REVERT: A 963 TYR cc_start: 0.9037 (OUTLIER) cc_final: 0.7926 (t80) outliers start: 13 outliers final: 10 residues processed: 56 average time/residue: 0.1973 time to fit residues: 16.9288 Evaluate side-chains 60 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 726 GLN Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 963 TYR Chi-restraints excluded: chain A residue 1064 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 87 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 85 optimal weight: 0.0270 chunk 8 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 67 optimal weight: 0.0770 chunk 12 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.097430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.076037 restraints weight = 26184.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.077214 restraints weight = 13941.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.077714 restraints weight = 10611.163| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3270 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3270 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 9614 Z= 0.130 Angle : 0.560 19.769 13391 Z= 0.270 Chirality : 0.038 0.209 1577 Planarity : 0.004 0.042 1461 Dihedral : 17.259 148.220 2204 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.45 % Allowed : 15.42 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.27), residues: 982 helix: 0.74 (0.26), residues: 447 sheet: 0.03 (0.53), residues: 111 loop : -1.34 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 542 HIS 0.002 0.000 HIS A 145 PHE 0.008 0.001 PHE A 950 TYR 0.011 0.001 TYR A 212 ARG 0.003 0.000 ARG A 144 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2884.77 seconds wall clock time: 51 minutes 10.59 seconds (3070.59 seconds total)