Starting phenix.real_space_refine on Fri Feb 14 02:35:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xjz_33238/02_2025/7xjz_33238.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xjz_33238/02_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_33238/02_2025/7xjz_33238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xjz_33238/02_2025/7xjz_33238.map" model { file = "/net/cci-nas-00/data/ceres_data/7xjz_33238/02_2025/7xjz_33238.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xjz_33238/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 8.84, per 1000 atoms: 0.95 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: 2.37 Conformation dependent library (CDL) restraints added in 2.1 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: 3.14 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: 3.59 Time building geometry restraints manager: 2.79 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: 1.040 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 30.490 Find NCS groups from input model: 0.090 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: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.740 ------------------------------------------------------------------------------- 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 : 0.897 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: 0.2666 time to fit residues: 40.0733 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 : 0.966 ------------------------------------------------------------------------------- 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 = 26272.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.077068 restraints weight = 13856.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.077657 restraints weight = 9867.902| |-----------------------------------------------------------------------------| 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 : 0.970 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: 0.4437 (OUTLIER) cc_final: 0.2792 (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: 0.7920 (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: 0.2000 time to fit residues: 22.8771 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 : 0.879 ------------------------------------------------------------------------------- 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: 7.9990 chunk 72 optimal weight: 0.0370 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 99 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 89 optimal weight: 20.0000 overall best weight: 1.1262 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.097209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.074501 restraints weight = 26722.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.076349 restraints weight = 14649.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.077568 restraints weight = 9557.633| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 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 = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1654 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= 0.159 Angle : 0.532 7.566 13391 Z= 0.267 Chirality : 0.039 0.174 1577 Planarity : 0.004 0.046 1461 Dihedral : 17.547 149.126 2211 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.65 % Allowed : 12.65 % Favored : 84.70 % 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: 445 sheet: -0.18 (0.53), residues: 112 loop : -1.62 (0.27), 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 274 PHE 0.007 0.001 PHE A 474 TYR 0.014 0.001 TYR A 230 ARG 0.007 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 77 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 55 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 ASN cc_start: 0.7945 (t0) cc_final: 0.7685 (t0) REVERT: A 267 MET cc_start: 0.9018 (mmm) cc_final: 0.8810 (mmp) REVERT: A 495 TYR cc_start: 0.4241 (OUTLIER) cc_final: 0.2628 (m-80) REVERT: A 597 MET cc_start: 0.8679 (tmm) cc_final: 0.8450 (tmm) REVERT: A 653 ASP cc_start: 0.7908 (p0) cc_final: 0.7668 (t0) REVERT: A 793 MET cc_start: 0.8835 (mmm) cc_final: 0.8518 (mmm) REVERT: A 875 ASN cc_start: 0.9075 (OUTLIER) cc_final: 0.8808 (m-40) REVERT: A 906 GLN cc_start: 0.7946 (tm-30) cc_final: 0.7563 (tm-30) REVERT: A 963 TYR cc_start: 0.8788 (OUTLIER) cc_final: 0.7986 (t80) REVERT: A 1052 VAL cc_start: 0.8226 (t) cc_final: 0.8016 (t) outliers start: 22 outliers final: 11 residues processed: 72 average time/residue: 0.2083 time to fit residues: 22.0448 Evaluate side-chains 65 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 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 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: 4.9990 chunk 21 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- 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 = 0.3597 r_free = 0.3597 target = 0.093983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.070974 restraints weight = 26690.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.072620 restraints weight = 15851.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.073709 restraints weight = 10865.418| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9614 Z= 0.347 Angle : 0.635 16.157 13391 Z= 0.318 Chirality : 0.043 0.156 1577 Planarity : 0.005 0.057 1461 Dihedral : 17.713 146.976 2210 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.53 % Allowed : 13.01 % Favored : 84.46 % 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: -1.03 (0.27), residues: 982 helix: 0.12 (0.26), residues: 445 sheet: -0.45 (0.51), residues: 120 loop : -1.60 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 198 HIS 0.004 0.001 HIS A 312 PHE 0.015 0.002 PHE A 544 TYR 0.024 0.002 TYR A 230 ARG 0.005 0.001 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 68 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 47 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: A 75 GLN cc_start: 0.9376 (OUTLIER) cc_final: 0.9092 (tm-30) REVERT: A 237 MET cc_start: 0.8413 (ttt) cc_final: 0.8177 (ttt) REVERT: A 263 ASN cc_start: 0.8045 (t0) cc_final: 0.7811 (t0) REVERT: A 495 TYR cc_start: 0.4828 (OUTLIER) cc_final: 0.2881 (m-80) REVERT: A 597 MET cc_start: 0.8818 (tmm) cc_final: 0.8584 (tmm) REVERT: A 726 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.7919 (tm-30) REVERT: A 743 MET cc_start: 0.8857 (mmt) cc_final: 0.8421 (mmm) REVERT: A 875 ASN cc_start: 0.9144 (OUTLIER) cc_final: 0.8782 (m-40) REVERT: A 963 TYR cc_start: 0.8953 (OUTLIER) cc_final: 0.7862 (t80) REVERT: A 1052 VAL cc_start: 0.8423 (t) cc_final: 0.8196 (t) outliers start: 21 outliers final: 11 residues processed: 63 average time/residue: 0.2166 time to fit residues: 19.9832 Evaluate side-chains 61 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 45 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLN 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 330 ARG 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: 0.7980 chunk 103 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 74 optimal weight: 0.0270 chunk 54 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 80 optimal weight: 0.0040 overall best weight: 0.7452 ------------------------------------------------------------------------------- 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 ** 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 = 0.3642 r_free = 0.3642 target = 0.096981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.074220 restraints weight = 26818.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.076036 restraints weight = 14653.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.077267 restraints weight = 9646.192| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 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 = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2017 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 : 0.530 12.179 13391 Z= 0.260 Chirality : 0.039 0.170 1577 Planarity : 0.004 0.045 1461 Dihedral : 17.516 147.121 2210 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.41 % Allowed : 13.25 % 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: -0.82 (0.27), residues: 982 helix: 0.30 (0.26), residues: 447 sheet: -0.25 (0.53), residues: 110 loop : -1.51 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 542 HIS 0.003 0.000 HIS A 145 PHE 0.009 0.001 PHE A 950 TYR 0.013 0.001 TYR A 230 ARG 0.005 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 76 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 1.015 Fit side-chains REVERT: A 263 ASN cc_start: 0.7821 (t0) cc_final: 0.7598 (t0) REVERT: A 495 TYR cc_start: 0.4797 (OUTLIER) cc_final: 0.2927 (m-80) REVERT: A 597 MET cc_start: 0.8760 (tmm) cc_final: 0.8528 (tmm) REVERT: A 653 ASP cc_start: 0.7941 (p0) cc_final: 0.7603 (t0) REVERT: A 726 GLN cc_start: 0.8025 (pp30) cc_final: 0.7694 (tm-30) REVERT: A 875 ASN cc_start: 0.9031 (OUTLIER) cc_final: 0.8819 (m-40) REVERT: A 906 GLN cc_start: 0.8005 (tm-30) cc_final: 0.7742 (tm-30) REVERT: A 963 TYR cc_start: 0.8871 (OUTLIER) cc_final: 0.7916 (t80) outliers start: 20 outliers final: 10 residues processed: 70 average time/residue: 0.2064 time to fit residues: 21.3470 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 : 1.067 ------------------------------------------------------------------------------- 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 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 1064 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 42 optimal weight: 0.8980 chunk 94 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 48 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 341 GLN ** 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 = 0.3621 r_free = 0.3621 target = 0.095868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.072971 restraints weight = 26764.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.074731 restraints weight = 14807.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.075948 restraints weight = 9820.601| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 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 = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2182 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= 0.187 Angle : 0.543 11.323 13391 Z= 0.267 Chirality : 0.039 0.158 1577 Planarity : 0.004 0.048 1461 Dihedral : 17.498 147.342 2210 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.29 % Allowed : 13.13 % 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: -0.77 (0.27), residues: 982 helix: 0.33 (0.26), residues: 447 sheet: -0.29 (0.53), residues: 112 loop : -1.46 (0.28), residues: 423 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 0.010 0.001 PHE A 950 TYR 0.016 0.001 TYR A 230 ARG 0.005 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 70 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 51 time to evaluate : 1.060 Fit side-chains REVERT: A 260 PHE cc_start: 0.8454 (m-80) cc_final: 0.8193 (m-80) REVERT: A 278 ASP cc_start: 0.7460 (p0) cc_final: 0.7152 (p0) REVERT: A 495 TYR cc_start: 0.4999 (OUTLIER) cc_final: 0.3002 (m-80) REVERT: A 597 MET cc_start: 0.8759 (tmm) cc_final: 0.8531 (tmm) REVERT: A 653 ASP cc_start: 0.7888 (p0) cc_final: 0.7669 (t0) REVERT: A 726 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7749 (tm-30) REVERT: A 743 MET cc_start: 0.8747 (mmt) cc_final: 0.8375 (mmm) REVERT: A 875 ASN cc_start: 0.9052 (OUTLIER) cc_final: 0.8829 (m-40) REVERT: A 906 GLN cc_start: 0.7939 (tm-30) cc_final: 0.7581 (tm-30) REVERT: A 947 MET cc_start: 0.8045 (ttp) cc_final: 0.7762 (ttp) REVERT: A 963 TYR cc_start: 0.9023 (OUTLIER) cc_final: 0.7949 (t80) outliers start: 19 outliers final: 11 residues processed: 64 average time/residue: 0.2010 time to fit residues: 19.5201 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 : 0.901 ------------------------------------------------------------------------------- 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 325 VAL 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 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: 2.9990 chunk 96 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 ASN ** 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 = 0.3642 r_free = 0.3642 target = 0.096451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.074924 restraints weight = 26415.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.076608 restraints weight = 14524.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.077129 restraints weight = 8947.733| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 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 = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2304 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= 0.142 Angle : 0.532 13.144 13391 Z= 0.257 Chirality : 0.039 0.158 1577 Planarity : 0.004 0.042 1461 Dihedral : 17.415 147.778 2210 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.93 % Allowed : 14.34 % Favored : 83.73 % 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: -0.67 (0.27), residues: 982 helix: 0.42 (0.26), residues: 448 sheet: -0.17 (0.53), residues: 111 loop : -1.43 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 542 HIS 0.003 0.001 HIS A 274 PHE 0.009 0.001 PHE A 986 TYR 0.013 0.001 TYR A 230 ARG 0.004 0.000 ARG A 330 *********************** 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 67 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: A 495 TYR cc_start: 0.4914 (OUTLIER) cc_final: 0.2960 (m-80) REVERT: A 597 MET cc_start: 0.8771 (tmm) cc_final: 0.8540 (tmm) REVERT: A 726 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7756 (tm-30) REVERT: A 743 MET cc_start: 0.8642 (mmt) cc_final: 0.8395 (mmm) REVERT: A 906 GLN cc_start: 0.7938 (tm-30) cc_final: 0.7594 (tm-30) REVERT: A 947 MET cc_start: 0.8020 (ttp) cc_final: 0.7742 (ttp) REVERT: A 963 TYR cc_start: 0.9001 (OUTLIER) cc_final: 0.7971 (t80) REVERT: A 1052 VAL cc_start: 0.8192 (t) cc_final: 0.7964 (t) outliers start: 16 outliers final: 12 residues processed: 62 average time/residue: 0.1784 time to fit residues: 17.2919 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 : 0.962 ------------------------------------------------------------------------------- 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 263 ASN 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 726 GLN Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 929 VAL 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: 6.9990 chunk 37 optimal weight: 0.3980 chunk 3 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 60 optimal weight: 0.0040 chunk 4 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 overall best weight: 0.8394 ------------------------------------------------------------------------------- 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 263 ASN ** 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 = 0.3655 r_free = 0.3655 target = 0.097629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.075904 restraints weight = 27243.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.077434 restraints weight = 14237.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.077891 restraints weight = 10770.390| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- 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: 0.8338 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9614 Z= 0.137 Angle : 0.534 14.947 13391 Z= 0.258 Chirality : 0.038 0.154 1577 Planarity : 0.004 0.042 1461 Dihedral : 17.368 148.160 2208 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.93 % Allowed : 14.82 % 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: -0.57 (0.27), residues: 982 helix: 0.52 (0.26), residues: 448 sheet: -0.13 (0.53), residues: 111 loop : -1.40 (0.28), residues: 423 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 0.010 0.001 PHE A 986 TYR 0.012 0.001 TYR A 230 ARG 0.004 0.000 ARG A 350 *********************** 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 66 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.918 Fit side-chains REVERT: A 160 GLN cc_start: 0.8496 (pt0) cc_final: 0.8153 (pt0) REVERT: A 278 ASP cc_start: 0.7529 (p0) cc_final: 0.7173 (p0) REVERT: A 495 TYR cc_start: 0.4808 (OUTLIER) cc_final: 0.2890 (m-80) REVERT: A 597 MET cc_start: 0.8741 (tmm) cc_final: 0.8506 (tmm) REVERT: A 726 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7781 (tm-30) REVERT: A 743 MET cc_start: 0.8631 (mmt) cc_final: 0.8377 (mmm) REVERT: A 906 GLN cc_start: 0.7931 (tm-30) cc_final: 0.7583 (tm-30) REVERT: A 947 MET cc_start: 0.8020 (ttp) cc_final: 0.7665 (ttp) REVERT: A 963 TYR cc_start: 0.8996 (OUTLIER) cc_final: 0.7969 (t80) REVERT: A 1052 VAL cc_start: 0.8152 (t) cc_final: 0.7921 (t) outliers start: 16 outliers final: 11 residues processed: 60 average time/residue: 0.1862 time to fit residues: 17.4848 Evaluate side-chains 63 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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 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 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: 8.9990 chunk 70 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 263 ASN ** 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 = 0.3601 r_free = 0.3601 target = 0.094158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.071367 restraints weight = 26343.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.073045 restraints weight = 15153.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.074142 restraints weight = 10268.879| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3172 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3172 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9614 Z= 0.273 Angle : 0.598 15.140 13391 Z= 0.294 Chirality : 0.041 0.154 1577 Planarity : 0.004 0.051 1461 Dihedral : 17.465 146.997 2208 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.81 % Allowed : 14.82 % Favored : 83.37 % 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: -0.62 (0.27), residues: 982 helix: 0.50 (0.26), residues: 447 sheet: -0.31 (0.53), residues: 113 loop : -1.42 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 198 HIS 0.003 0.001 HIS A 312 PHE 0.012 0.001 PHE A 544 TYR 0.022 0.002 TYR A 230 ARG 0.005 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 60 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.984 Fit side-chains REVERT: A 263 ASN cc_start: 0.7514 (OUTLIER) cc_final: 0.6981 (t0) REVERT: A 495 TYR cc_start: 0.4929 (OUTLIER) cc_final: 0.2975 (m-80) REVERT: A 597 MET cc_start: 0.8799 (tmm) cc_final: 0.8566 (tmm) REVERT: A 726 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7867 (tm-30) REVERT: A 743 MET cc_start: 0.8794 (mmt) cc_final: 0.8494 (mmm) REVERT: A 947 MET cc_start: 0.8075 (ttp) cc_final: 0.7748 (ttp) REVERT: A 963 TYR cc_start: 0.9054 (OUTLIER) cc_final: 0.7854 (t80) outliers start: 15 outliers final: 10 residues processed: 55 average time/residue: 0.1848 time to fit residues: 16.3706 Evaluate side-chains 59 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 85 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 83 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 45 optimal weight: 0.2980 chunk 14 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 263 ASN ** 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 = 0.3654 r_free = 0.3654 target = 0.097102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.075437 restraints weight = 26800.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.077134 restraints weight = 14911.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.077550 restraints weight = 9392.426| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 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 = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9614 Z= 0.133 Angle : 0.542 15.740 13391 Z= 0.262 Chirality : 0.038 0.152 1577 Planarity : 0.004 0.045 1461 Dihedral : 17.380 147.056 2208 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.57 % Allowed : 15.18 % 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: -0.45 (0.27), residues: 982 helix: 0.63 (0.26), residues: 451 sheet: -0.13 (0.54), residues: 109 loop : -1.35 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 542 HIS 0.003 0.000 HIS A 145 PHE 0.011 0.001 PHE A 986 TYR 0.012 0.001 TYR A 230 ARG 0.004 0.000 ARG A 350 ********************** 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 60 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.921 Fit side-chains REVERT: A 160 GLN cc_start: 0.8537 (pt0) cc_final: 0.8320 (pt0) REVERT: A 263 ASN cc_start: 0.8249 (OUTLIER) cc_final: 0.7840 (t0) REVERT: A 495 TYR cc_start: 0.4925 (OUTLIER) cc_final: 0.3049 (m-80) REVERT: A 597 MET cc_start: 0.8802 (tmm) cc_final: 0.8564 (tmm) REVERT: A 726 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7839 (tm-30) REVERT: A 743 MET cc_start: 0.8681 (mmt) cc_final: 0.8397 (mmm) REVERT: A 947 MET cc_start: 0.8028 (ttp) cc_final: 0.7733 (ttp) REVERT: A 963 TYR cc_start: 0.9040 (OUTLIER) cc_final: 0.7909 (t80) outliers start: 13 outliers final: 9 residues processed: 54 average time/residue: 0.1927 time to fit residues: 16.3295 Evaluate side-chains 59 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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 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 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: 0.6980 chunk 32 optimal weight: 0.0770 chunk 85 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 67 optimal weight: 0.0470 chunk 12 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.097583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.074638 restraints weight = 26705.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.076586 restraints weight = 14205.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.077873 restraints weight = 9149.665| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3243 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 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 = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3243 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9614 Z= 0.125 Angle : 0.533 15.798 13391 Z= 0.256 Chirality : 0.038 0.148 1577 Planarity : 0.004 0.042 1461 Dihedral : 17.317 147.674 2208 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.69 % Allowed : 15.06 % 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: -0.38 (0.27), residues: 982 helix: 0.70 (0.26), residues: 448 sheet: -0.02 (0.53), residues: 111 loop : -1.35 (0.28), residues: 423 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 0.010 0.001 PHE A 986 TYR 0.013 0.001 TYR A 212 ARG 0.004 0.000 ARG A 330 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2832.84 seconds wall clock time: 51 minutes 16.55 seconds (3076.55 seconds total)