Starting phenix.real_space_refine on Fri Sep 11 13:51:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xjz_33238/09_2026/7xjz_33238.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xjz_33238/09_2026/7xjz_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7xjz_33238/09_2026/7xjz_33238.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xjz_33238/09_2026/7xjz_33238.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xjz_33238/09_2026/7xjz_33238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xjz_33238/09_2026/7xjz_33238.map" model { file = "/net/cci-nas-00/data/ceres_data/7xjz_33238/09_2026/7xjz_33238.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xjz_33238/09_2026/7xjz_33238.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.073 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ARG:plan': 4, 'GLU:plan': 7, 'ASP:plan': 2, 'GLN:plan1': 1} 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: {'ARG:plan': 4, 'GLU:plan': 7, 'ASP:plan': 2, 'GLN:plan1': 1} 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: {'RNAv2': 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: 3.35, per 1000 atoms: 0.36 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: 0.79 Conformation dependent library (CDL) restraints added in 739.0 milliseconds 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: 1.00 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: 1.97 Time building geometry restraints manager: 1.08 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: 12970 1.83 - 3.66: 360 3.66 - 5.49: 47 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 - 19.67: 5167 19.67 - 39.35: 330 39.35 - 59.02: 120 59.02 - 78.69: 18 78.69 - 98.37: 4 Dihedral angle restraints: 5639 sinusoidal: 2781 harmonic: 2858 Sorted by residual: dihedral pdb=" C4' G B 17 " pdb=" C3' G B 17 " pdb=" C2' G B 17 " pdb=" C1' G B 17 " ideal model delta sinusoidal sigma weight residual 36.34 -36.55 72.89 1 3.10e+00 1.04e-01 7.05e+02 dihedral pdb=" C4' U B 46 " pdb=" C3' U B 46 " pdb=" C2' U B 46 " pdb=" C1' U B 46 " ideal model delta sinusoidal sigma weight residual 36.34 -35.74 72.09 1 3.10e+00 1.04e-01 6.92e+02 dihedral pdb=" C4' U B 32 " pdb=" C3' U B 32 " pdb=" C2' U B 32 " pdb=" C1' U B 32 " ideal model delta sinusoidal sigma weight residual 36.35 -35.54 71.89 1 3.10e+00 1.04e-01 6.88e+02 ... (remaining 5636 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1268 0.057 - 0.113: 198 0.113 - 0.170: 20 0.170 - 0.226: 15 0.226 - 0.283: 76 Chirality restraints: 1577 Sorted by residual: chirality pdb=" C2' U B 46 " pdb=" C3' U B 46 " pdb=" O2' U B 46 " pdb=" C1' U B 46 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C2' U B 31 " pdb=" C3' U B 31 " pdb=" O2' U B 31 " pdb=" C1' U B 31 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C2' U B 58 " pdb=" C3' U B 58 " pdb=" O2' U B 58 " pdb=" C1' U B 58 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.27 2.00e-01 2.50e+01 1.89e+00 ... (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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.560 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 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 0.176 9615 Z= 0.269 Angle : 0.696 9.148 13391 Z= 0.346 Chirality : 0.070 0.283 1577 Planarity : 0.004 0.043 1461 Dihedral : 14.611 98.366 3791 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (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 ARG 0.002 0.000 ARG A1045 TYR 0.012 0.001 TYR A 230 PHE 0.010 0.001 PHE A 544 TRP 0.008 0.001 TRP A 194 HIS 0.004 0.001 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.20 ( 9614) covalent geometry : angle 0.69642 / 0.35 (13391) hydrogen bonds : bond 0.16244 / 10.76 ( 369) hydrogen bonds : angle 7.42555 / 4.98 ( 1013) Misc. bond : bond 0.17590 / 9.26 ( 1) *********************** 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 : 0.321 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: 0.7515 (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: 0.1147 time to fit residues: 17.4099 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 : 0.377 ------------------------------------------------------------------------------- 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 49 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.0070 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3677 r_free = 0.3677 target = 0.098769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.076606 restraints weight = 26332.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.078468 restraints weight = 13749.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.078917 restraints weight = 9509.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.079026 restraints weight = 7228.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.079766 restraints weight = 7083.636| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3272 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3272 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9615 Z= 0.133 Angle : 0.833 13.812 13391 Z= 0.361 Chirality : 0.068 0.889 1577 Planarity : 0.004 0.040 1461 Dihedral : 13.854 151.314 1959 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.89 % Allowed : 11.93 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.27), residues: 982 helix: 0.17 (0.26), residues: 448 sheet: -0.09 (0.53), residues: 110 loop : -1.63 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 927 TYR 0.012 0.001 TYR A 230 PHE 0.024 0.001 PHE A 260 TRP 0.007 0.001 TRP A 542 HIS 0.003 0.001 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 ( 9614) covalent geometry : angle 0.83267 / 0.36 (13391) hydrogen bonds : bond 0.04095 / 2.61 ( 369) hydrogen bonds : angle 4.22127 / 2.98 ( 1013) Misc. bond : bond 0.00117 / 0.06 ( 1) *********************** 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 83 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 59 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 93 MET cc_start: 0.7879 (mtm) cc_final: 0.7656 (mtp) REVERT: A 237 MET cc_start: 0.8246 (ttt) cc_final: 0.7990 (ttt) REVERT: A 263 ASN cc_start: 0.7877 (t0) cc_final: 0.7544 (t0) REVERT: A 267 MET cc_start: 0.8968 (mmm) cc_final: 0.8714 (mmp) REVERT: A 495 TYR cc_start: 0.4288 (OUTLIER) cc_final: 0.2736 (m-80) REVERT: A 597 MET cc_start: 0.8661 (tmm) cc_final: 0.8455 (tmm) REVERT: A 653 ASP cc_start: 0.7865 (p0) cc_final: 0.7578 (t0) REVERT: A 714 MET cc_start: 0.8394 (tmm) cc_final: 0.8083 (tmm) REVERT: A 726 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7612 (pp30) REVERT: A 775 MET cc_start: 0.8126 (tmm) cc_final: 0.7920 (tmm) REVERT: A 793 MET cc_start: 0.8759 (mmm) cc_final: 0.8444 (mmm) REVERT: A 875 ASN cc_start: 0.9050 (OUTLIER) cc_final: 0.8791 (m-40) REVERT: A 906 GLN cc_start: 0.8003 (tm-30) cc_final: 0.7659 (tm-30) REVERT: A 963 TYR cc_start: 0.8739 (OUTLIER) cc_final: 0.8058 (t80) outliers start: 24 outliers final: 8 residues processed: 78 average time/residue: 0.0846 time to fit residues: 9.9201 Evaluate side-chains 67 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 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 29 optimal weight: 0.0870 chunk 10 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 90 optimal weight: 0.5980 chunk 98 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3680 r_free = 0.3680 target = 0.099124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.077137 restraints weight = 26561.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.078995 restraints weight = 13617.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.079548 restraints weight = 9329.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.079687 restraints weight = 7051.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.079794 restraints weight = 7041.411| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3275 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3275 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9615 Z= 0.109 Angle : 0.676 12.225 13391 Z= 0.302 Chirality : 0.055 0.455 1577 Planarity : 0.004 0.041 1461 Dihedral : 13.745 155.533 1955 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.93 % Allowed : 12.89 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.27), residues: 982 helix: 0.27 (0.26), residues: 449 sheet: -0.16 (0.53), residues: 110 loop : -1.61 (0.27), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 144 TYR 0.011 0.001 TYR A 230 PHE 0.007 0.001 PHE A 474 TRP 0.008 0.001 TRP A 542 HIS 0.004 0.001 HIS A 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 ( 9614) covalent geometry : angle 0.67624 / 0.30 (13391) hydrogen bonds : bond 0.03384 / 2.17 ( 369) hydrogen bonds : angle 4.02334 / 2.82 ( 1013) Misc. bond : bond 0.00062 / 0.03 ( 1) *********************** 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 74 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 263 ASN cc_start: 0.7912 (t0) cc_final: 0.7626 (t0) REVERT: A 267 MET cc_start: 0.8987 (mmm) cc_final: 0.8756 (mmp) REVERT: A 495 TYR cc_start: 0.4244 (OUTLIER) cc_final: 0.2706 (m-80) REVERT: A 597 MET cc_start: 0.8678 (tmm) cc_final: 0.8396 (tmm) REVERT: A 726 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7689 (pp30) REVERT: A 793 MET cc_start: 0.8786 (mmm) cc_final: 0.8487 (mmm) REVERT: A 875 ASN cc_start: 0.9030 (OUTLIER) cc_final: 0.8810 (m-40) REVERT: A 906 GLN cc_start: 0.7952 (tm-30) cc_final: 0.7543 (tm-30) REVERT: A 963 TYR cc_start: 0.8768 (OUTLIER) cc_final: 0.8043 (t80) REVERT: A 1052 VAL cc_start: 0.8223 (t) cc_final: 0.8011 (t) outliers start: 16 outliers final: 8 residues processed: 69 average time/residue: 0.0880 time to fit residues: 9.0288 Evaluate side-chains 65 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3648 r_free = 0.3648 target = 0.097290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.073654 restraints weight = 26194.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.075548 restraints weight = 14267.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.076836 restraints weight = 9268.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.077686 restraints weight = 6824.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.078221 restraints weight = 5503.136| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3276 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3276 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 9615 Z= 0.113 Angle : 0.668 15.436 13391 Z= 0.300 Chirality : 0.053 0.367 1577 Planarity : 0.004 0.043 1461 Dihedral : 13.737 158.857 1954 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.41 % Allowed : 13.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.27), residues: 982 helix: 0.36 (0.26), residues: 447 sheet: -0.13 (0.52), residues: 111 loop : -1.62 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 144 TYR 0.012 0.001 TYR A 230 PHE 0.025 0.001 PHE A 986 TRP 0.008 0.001 TRP A 542 HIS 0.002 0.000 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 9614) covalent geometry : angle 0.66836 / 0.30 (13391) hydrogen bonds : bond 0.03282 / 2.11 ( 369) hydrogen bonds : angle 3.92188 / 2.75 ( 1013) Misc. bond : bond 0.00062 / 0.03 ( 1) *********************** 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 73 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 53 time to evaluate : 0.329 Fit side-chains REVERT: A 160 GLN cc_start: 0.8611 (pt0) cc_final: 0.8367 (pt0) REVERT: A 237 MET cc_start: 0.8216 (ttt) cc_final: 0.7964 (ttt) REVERT: A 263 ASN cc_start: 0.7871 (t0) cc_final: 0.7622 (t0) REVERT: A 267 MET cc_start: 0.9003 (mmm) cc_final: 0.8798 (mmp) REVERT: A 278 ASP cc_start: 0.7244 (p0) cc_final: 0.6958 (p0) REVERT: A 495 TYR cc_start: 0.4193 (OUTLIER) cc_final: 0.2641 (m-80) REVERT: A 597 MET cc_start: 0.8703 (tmm) cc_final: 0.8417 (tmm) REVERT: A 743 MET cc_start: 0.8729 (mmt) cc_final: 0.8361 (mmm) REVERT: A 793 MET cc_start: 0.8773 (mmm) cc_final: 0.8563 (mmm) REVERT: A 875 ASN cc_start: 0.9089 (OUTLIER) cc_final: 0.8829 (m-40) REVERT: A 947 MET cc_start: 0.7717 (ttp) cc_final: 0.7494 (ttp) REVERT: A 963 TYR cc_start: 0.8771 (OUTLIER) cc_final: 0.7955 (t80) REVERT: A 1052 VAL cc_start: 0.8096 (t) cc_final: 0.7858 (t) outliers start: 20 outliers final: 9 residues processed: 68 average time/residue: 0.0874 time to fit residues: 8.8030 Evaluate side-chains 62 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 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 22 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 97 optimal weight: 7.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 906 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.096941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.073261 restraints weight = 26163.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.075123 restraints weight = 14355.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.076355 restraints weight = 9392.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.077186 restraints weight = 6974.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.077743 restraints weight = 5661.010| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3264 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3264 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9615 Z= 0.113 Angle : 0.647 11.989 13391 Z= 0.289 Chirality : 0.051 0.316 1577 Planarity : 0.004 0.042 1461 Dihedral : 13.546 161.453 1952 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.41 % Allowed : 13.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.27), residues: 982 helix: 0.52 (0.26), residues: 446 sheet: -0.05 (0.52), residues: 111 loop : -1.48 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 538 TYR 0.013 0.001 TYR A 230 PHE 0.008 0.001 PHE A 723 TRP 0.007 0.001 TRP A 542 HIS 0.003 0.001 HIS A 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 9614) covalent geometry : angle 0.64728 / 0.29 (13391) hydrogen bonds : bond 0.03293 / 2.13 ( 369) hydrogen bonds : angle 3.83337 / 2.69 ( 1013) Misc. bond : bond 0.00062 / 0.03 ( 1) *********************** 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 72 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 52 time to evaluate : 0.352 Fit side-chains REVERT: A 160 GLN cc_start: 0.8580 (pt0) cc_final: 0.8192 (pt0) REVERT: A 263 ASN cc_start: 0.7838 (t0) cc_final: 0.7548 (t0) REVERT: A 495 TYR cc_start: 0.4250 (OUTLIER) cc_final: 0.2641 (m-80) REVERT: A 597 MET cc_start: 0.8719 (tmm) cc_final: 0.8436 (tmm) REVERT: A 726 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7917 (tm-30) REVERT: A 875 ASN cc_start: 0.9084 (OUTLIER) cc_final: 0.8847 (m-40) REVERT: A 947 MET cc_start: 0.7832 (ttp) cc_final: 0.7584 (ttp) REVERT: A 963 TYR cc_start: 0.8819 (OUTLIER) cc_final: 0.7881 (t80) REVERT: A 1052 VAL cc_start: 0.8113 (t) cc_final: 0.7860 (t) outliers start: 20 outliers final: 9 residues processed: 65 average time/residue: 0.0850 time to fit residues: 8.4028 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 : 0.247 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 90 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 102 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 HIS A 341 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.097400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.073779 restraints weight = 26281.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.075600 restraints weight = 14339.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.076903 restraints weight = 9348.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.077700 restraints weight = 6910.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.078278 restraints weight = 5607.806| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3269 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3269 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9615 Z= 0.106 Angle : 0.639 12.762 13391 Z= 0.284 Chirality : 0.050 0.271 1577 Planarity : 0.004 0.041 1461 Dihedral : 13.399 162.936 1950 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.93 % Allowed : 13.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.27), residues: 982 helix: 0.54 (0.26), residues: 447 sheet: -0.07 (0.52), residues: 111 loop : -1.45 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 144 TYR 0.013 0.001 TYR A 230 PHE 0.008 0.001 PHE A 986 TRP 0.008 0.001 TRP A 542 HIS 0.002 0.000 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 9614) covalent geometry : angle 0.63869 / 0.28 (13391) hydrogen bonds : bond 0.03167 / 2.04 ( 369) hydrogen bonds : angle 3.79788 / 2.66 ( 1013) Misc. bond : bond 0.00057 / 0.03 ( 1) *********************** 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 68 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: A 263 ASN cc_start: 0.7709 (t0) cc_final: 0.7509 (t0) REVERT: A 495 TYR cc_start: 0.4363 (OUTLIER) cc_final: 0.2725 (m-80) REVERT: A 597 MET cc_start: 0.8721 (tmm) cc_final: 0.8445 (tmm) REVERT: A 726 GLN cc_start: 0.7944 (pp30) cc_final: 0.7727 (tm-30) REVERT: A 743 MET cc_start: 0.8655 (mmt) cc_final: 0.8435 (mmm) REVERT: A 875 ASN cc_start: 0.9077 (OUTLIER) cc_final: 0.8869 (m-40) REVERT: A 947 MET cc_start: 0.7911 (ttp) cc_final: 0.7706 (ttp) REVERT: A 963 TYR cc_start: 0.8823 (OUTLIER) cc_final: 0.7886 (t80) outliers start: 16 outliers final: 9 residues processed: 63 average time/residue: 0.0947 time to fit residues: 8.7937 Evaluate side-chains 60 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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 436 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 963 TYR Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1064 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 69 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.096969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.073403 restraints weight = 26248.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.075270 restraints weight = 14382.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.076521 restraints weight = 9413.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.077336 restraints weight = 6968.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.077883 restraints weight = 5663.284| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 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 = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9615 Z= 0.112 Angle : 0.642 14.643 13391 Z= 0.286 Chirality : 0.050 0.270 1577 Planarity : 0.004 0.042 1461 Dihedral : 13.347 164.065 1950 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.81 % Allowed : 13.86 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.27), residues: 982 helix: 0.66 (0.26), residues: 448 sheet: -0.04 (0.53), residues: 111 loop : -1.41 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 144 TYR 0.014 0.001 TYR A 230 PHE 0.008 0.001 PHE A 950 TRP 0.007 0.001 TRP A 542 HIS 0.002 0.000 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 9614) covalent geometry : angle 0.64245 / 0.29 (13391) hydrogen bonds : bond 0.03246 / 2.10 ( 369) hydrogen bonds : angle 3.76416 / 2.64 ( 1013) Misc. bond : bond 0.00060 / 0.03 ( 1) *********************** 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 64 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.322 Fit side-chains REVERT: A 160 GLN cc_start: 0.8593 (pt0) cc_final: 0.8318 (pt0) REVERT: A 263 ASN cc_start: 0.7826 (t0) cc_final: 0.7612 (t0) REVERT: A 495 TYR cc_start: 0.4307 (OUTLIER) cc_final: 0.2584 (m-80) REVERT: A 597 MET cc_start: 0.8766 (tmm) cc_final: 0.8502 (tmm) REVERT: A 726 GLN cc_start: 0.8143 (pp30) cc_final: 0.7933 (tm-30) REVERT: A 743 MET cc_start: 0.8789 (mmt) cc_final: 0.8464 (mmm) REVERT: A 875 ASN cc_start: 0.9123 (OUTLIER) cc_final: 0.8874 (m-40) REVERT: A 947 MET cc_start: 0.7912 (ttp) cc_final: 0.7694 (ttp) REVERT: A 963 TYR cc_start: 0.8939 (OUTLIER) cc_final: 0.7828 (t80) outliers start: 15 outliers final: 8 residues processed: 59 average time/residue: 0.0774 time to fit residues: 7.1796 Evaluate side-chains 58 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 436 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 963 TYR Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1064 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 3 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 101 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 73 optimal weight: 0.0070 chunk 57 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 5 optimal weight: 0.4980 chunk 80 optimal weight: 5.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.098659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.075018 restraints weight = 26289.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.076889 restraints weight = 14298.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.078210 restraints weight = 9334.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.079064 restraints weight = 6933.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.079616 restraints weight = 5621.060| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3285 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3285 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9615 Z= 0.098 Angle : 0.631 13.877 13391 Z= 0.282 Chirality : 0.049 0.260 1577 Planarity : 0.004 0.040 1461 Dihedral : 13.278 165.483 1950 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.45 % Allowed : 14.70 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.27), residues: 982 helix: 0.77 (0.26), residues: 451 sheet: -0.10 (0.52), residues: 113 loop : -1.42 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 144 TYR 0.013 0.001 TYR A 212 PHE 0.007 0.001 PHE A 474 TRP 0.009 0.001 TRP A 542 HIS 0.002 0.000 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 ( 9614) covalent geometry : angle 0.63098 / 0.28 (13391) hydrogen bonds : bond 0.02986 / 1.89 ( 369) hydrogen bonds : angle 3.73038 / 2.59 ( 1013) Misc. bond : bond 0.00060 / 0.03 ( 1) *********************** 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 67 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.325 Fit side-chains REVERT: A 160 GLN cc_start: 0.8546 (pt0) cc_final: 0.8226 (pt0) REVERT: A 263 ASN cc_start: 0.7827 (t0) cc_final: 0.7612 (t0) REVERT: A 495 TYR cc_start: 0.3920 (OUTLIER) cc_final: 0.2220 (m-80) REVERT: A 597 MET cc_start: 0.8757 (tmm) cc_final: 0.8483 (tmm) REVERT: A 743 MET cc_start: 0.8701 (mmt) cc_final: 0.8424 (mmm) REVERT: A 875 ASN cc_start: 0.9095 (OUTLIER) cc_final: 0.8823 (m-40) REVERT: A 947 MET cc_start: 0.7944 (ttp) cc_final: 0.7724 (ttp) REVERT: A 963 TYR cc_start: 0.8905 (OUTLIER) cc_final: 0.7803 (t80) outliers start: 12 outliers final: 8 residues processed: 63 average time/residue: 0.0763 time to fit residues: 7.5555 Evaluate side-chains 61 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 436 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 963 TYR Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1064 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 22 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 78 optimal weight: 0.0770 chunk 34 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 86 optimal weight: 9.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.098601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.076176 restraints weight = 26454.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.077445 restraints weight = 14059.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.078014 restraints weight = 10449.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.078373 restraints weight = 8281.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.078448 restraints weight = 7682.412| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3261 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 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 = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3261 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9615 Z= 0.101 Angle : 0.646 15.131 13391 Z= 0.289 Chirality : 0.049 0.259 1577 Planarity : 0.004 0.040 1461 Dihedral : 13.240 166.457 1950 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.33 % Allowed : 15.06 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.27), residues: 982 helix: 0.85 (0.26), residues: 451 sheet: -0.00 (0.52), residues: 111 loop : -1.41 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 144 TYR 0.011 0.001 TYR A 230 PHE 0.007 0.001 PHE A 474 TRP 0.008 0.001 TRP A 542 HIS 0.002 0.000 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 ( 9614) covalent geometry : angle 0.64616 / 0.29 (13391) hydrogen bonds : bond 0.02962 / 1.90 ( 369) hydrogen bonds : angle 3.70593 / 2.57 ( 1013) Misc. bond : bond 0.00061 / 0.03 ( 1) *********************** 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: 11 poor density : 49 time to evaluate : 0.266 Fit side-chains REVERT: A 160 GLN cc_start: 0.8540 (pt0) cc_final: 0.8282 (pt0) REVERT: A 495 TYR cc_start: 0.3947 (OUTLIER) cc_final: 0.2299 (m-80) REVERT: A 597 MET cc_start: 0.8764 (tmm) cc_final: 0.8491 (tmm) REVERT: A 743 MET cc_start: 0.8750 (mmt) cc_final: 0.8429 (mmm) REVERT: A 875 ASN cc_start: 0.9084 (OUTLIER) cc_final: 0.8845 (m-40) REVERT: A 963 TYR cc_start: 0.8953 (OUTLIER) cc_final: 0.7852 (t80) outliers start: 11 outliers final: 8 residues processed: 56 average time/residue: 0.0760 time to fit residues: 6.7001 Evaluate side-chains 57 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 436 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 963 TYR Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1064 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 24 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 93 optimal weight: 0.2980 chunk 100 optimal weight: 9.9990 chunk 50 optimal weight: 0.1980 chunk 73 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 48 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 263 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.099164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.076604 restraints weight = 26402.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.078188 restraints weight = 14217.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.078744 restraints weight = 10291.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.079057 restraints weight = 7960.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.079144 restraints weight = 7745.015| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3270 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3270 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9615 Z= 0.098 Angle : 0.645 15.543 13391 Z= 0.288 Chirality : 0.049 0.256 1577 Planarity : 0.004 0.039 1461 Dihedral : 13.206 167.314 1950 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.45 % Allowed : 15.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.27), residues: 982 helix: 0.87 (0.26), residues: 451 sheet: -0.02 (0.52), residues: 111 loop : -1.39 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 144 TYR 0.010 0.001 TYR A 230 PHE 0.007 0.001 PHE A 474 TRP 0.008 0.001 TRP A 542 HIS 0.002 0.000 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 ( 9614) covalent geometry : angle 0.64456 / 0.29 (13391) hydrogen bonds : bond 0.02902 / 1.85 ( 369) hydrogen bonds : angle 3.69100 / 2.56 ( 1013) Misc. bond : bond 0.00062 / 0.03 ( 1) ********************** 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 59 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.326 Fit side-chains REVERT: A 160 GLN cc_start: 0.8458 (pt0) cc_final: 0.8217 (pt0) REVERT: A 495 TYR cc_start: 0.3946 (OUTLIER) cc_final: 0.2418 (m-80) REVERT: A 597 MET cc_start: 0.8730 (tmm) cc_final: 0.8469 (tmm) REVERT: A 743 MET cc_start: 0.8729 (mmt) cc_final: 0.8419 (mmm) REVERT: A 963 TYR cc_start: 0.8971 (OUTLIER) cc_final: 0.7869 (t80) outliers start: 12 outliers final: 8 residues processed: 55 average time/residue: 0.0769 time to fit residues: 6.6734 Evaluate side-chains 56 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.288 ------------------------------------------------------------------------------- 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 414 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 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 58 optimal weight: 0.8980 chunk 100 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 93 optimal weight: 0.0570 chunk 7 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 91 optimal weight: 8.9990 chunk 104 optimal weight: 9.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 263 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.098752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.075066 restraints weight = 26254.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.077005 restraints weight = 14345.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.078244 restraints weight = 9391.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.079093 restraints weight = 6973.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.079644 restraints weight = 5677.264| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3296 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3296 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9615 Z= 0.101 Angle : 0.647 15.728 13391 Z= 0.289 Chirality : 0.049 0.256 1577 Planarity : 0.004 0.040 1461 Dihedral : 13.178 167.479 1948 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.20 % Allowed : 15.18 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.27), residues: 982 helix: 0.90 (0.26), residues: 451 sheet: -0.02 (0.52), residues: 111 loop : -1.38 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 144 TYR 0.010 0.001 TYR A 230 PHE 0.007 0.001 PHE A 474 TRP 0.008 0.001 TRP A 542 HIS 0.002 0.000 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 9614) covalent geometry : angle 0.64714 / 0.29 (13391) hydrogen bonds : bond 0.02936 / 1.86 ( 369) hydrogen bonds : angle 3.68952 / 2.56 ( 1013) Misc. bond : bond 0.00061 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1578.96 seconds wall clock time: 27 minutes 56.14 seconds (1676.14 seconds total)