Starting phenix.real_space_refine on Thu Mar 14 16:48:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjz_33238/03_2024/7xjz_33238_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjz_33238/03_2024/7xjz_33238.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjz_33238/03_2024/7xjz_33238.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjz_33238/03_2024/7xjz_33238.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjz_33238/03_2024/7xjz_33238_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjz_33238/03_2024/7xjz_33238_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.073 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 75 5.49 5 S 31 5.16 5 C 5618 2.51 5 N 1594 2.21 5 O 1958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 712": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 880": "OD1" <-> "OD2" Residue "A GLU 961": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9276 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7716 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 983, 7711 Classifications: {'peptide': 983} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 3, 'PTRANS': 43, 'TRANS': 936} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 58 Conformer: "B" Number of residues, atoms: 983, 7711 Classifications: {'peptide': 983} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 3, 'PTRANS': 43, 'TRANS': 936} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 58 bond proxies already assigned to first conformer: 7862 Chain: "B" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1560 Unusual residues: {'GTP': 1} Classifications: {'RNA': 72, 'undetermined': 1} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 31, 'rna3p_pyr': 33} Link IDs: {'rna2p': 8, 'rna3p': 63, None: 1} Not linked: pdbres="GTP B 1 " pdbres=" C B 2 " Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AALA A 940 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA A 940 " occ=0.50 Time building chain proxies: 8.85, per 1000 atoms: 0.95 Number of scatterers: 9276 At special positions: 0 Unit cell: (123.2, 107.8, 106.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 31 16.00 P 75 15.00 O 1958 8.00 N 1594 7.00 C 5618 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 4.16 Conformation dependent library (CDL) restraints added in 2.1 seconds 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1848 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 39 helices and 4 sheets defined 46.8% alpha, 8.4% beta 16 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 4.25 Creating SS restraints... Processing helix chain 'A' and resid 74 through 88 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) Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 159 through 170 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) Processing helix chain 'A' and resid 232 through 239 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 262 through 273 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) Processing helix chain 'A' and resid 277 through 297 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) removed outlier: 3.527A pdb=" N LEU A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 320 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 327 through 353 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) removed outlier: 4.257A pdb=" N LEU A 353 " --> pdb=" O THR A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 417 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 457 through 460 No H-bonds generated for 'chain 'A' and resid 457 through 460' Processing helix chain 'A' and resid 469 through 478 Processing helix chain 'A' and resid 482 through 484 No H-bonds generated for 'chain 'A' and resid 482 through 484' Processing helix chain 'A' and resid 509 through 520 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 585 through 590 removed outlier: 3.572A pdb=" N GLU A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 612 removed outlier: 4.282A pdb=" N LYS A 601 " --> pdb=" O MET A 597 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN A 602 " --> pdb=" O GLN A 598 " (cutoff:3.500A) 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) Processing helix chain 'A' and resid 623 through 632 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) removed outlier: 3.723A pdb=" N LEU A 632 " --> pdb=" O GLU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 648 Processing helix chain 'A' and resid 652 through 661 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) Processing helix chain 'A' and resid 690 through 715 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 720 through 724 removed outlier: 3.913A pdb=" N ARG A 724 " --> pdb=" O LEU A 720 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 720 through 724' Processing helix chain 'A' and resid 726 through 729 removed outlier: 4.300A pdb=" N SER A 729 " --> pdb=" O GLN A 726 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 726 through 729' Processing helix chain 'A' and resid 739 through 756 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 761 through 772 Proline residue: A 765 - end of helix removed outlier: 4.441A pdb=" N ALA A 771 " --> pdb=" O LYS A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 779 No H-bonds generated for 'chain 'A' and resid 777 through 779' Processing helix chain 'A' and resid 782 through 785 No H-bonds generated for 'chain 'A' and resid 782 through 785' Processing helix chain 'A' and resid 787 through 789 No H-bonds generated for 'chain 'A' and resid 787 through 789' Processing helix chain 'A' and resid 793 through 801 Processing helix chain 'A' and resid 805 through 814 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) removed outlier: 3.576A pdb=" N ILE A 814 " --> pdb=" O ALA A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 847 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) Processing helix chain 'A' and resid 861 through 873 Processing helix chain 'A' and resid 881 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 898 through 918 removed outlier: 3.848A pdb=" N ASP A 902 " --> pdb=" O SER A 898 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP A 918 " --> pdb=" O GLN A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 929 removed outlier: 3.580A pdb=" N SER A 928 " --> pdb=" O GLU A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 952 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) removed outlier: 4.037A pdb=" N ARG A 952 " --> pdb=" O GLU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 970 removed outlier: 3.754A pdb=" N SER A 964 " --> pdb=" O VAL A 960 " (cutoff:3.500A) Proline residue: A 966 - end of helix removed outlier: 4.206A pdb=" N ILE A 969 " --> pdb=" O ARG A 965 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 970 " --> pdb=" O PRO A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 977 No H-bonds generated for 'chain 'A' and resid 975 through 977' Processing helix chain 'A' and resid 989 through 1003 removed outlier: 3.856A pdb=" N ASP A1003 " --> pdb=" O LEU A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1031 removed outlier: 4.962A pdb=" N GLU A1020 " --> pdb=" O ASP A1016 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU A1021 " --> pdb=" O ALA A1017 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU A1022 " --> pdb=" O SER A1018 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLN A1023 " --> pdb=" O LEU A1019 " (cutoff:3.500A) Proline residue: A1024 - end of helix removed outlier: 3.926A pdb=" N ASP A1027 " --> pdb=" O GLN A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1053 Processing sheet with id= A, first strand: chain 'A' and resid 119 through 128 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= B, 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) Processing sheet with id= C, first strand: chain 'A' and resid 617 through 619 Processing sheet with id= D, first strand: chain 'A' and resid 636 through 642 removed outlier: 4.023A pdb=" N MET A 637 " --> pdb=" O ALA A 684 " (cutoff:3.500A) 269 hydrogen bonds defined for protein. 778 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 44 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 3.36 Time building geometry restraints manager: 4.18 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: 100.21 - 106.97: 649 106.97 - 113.72: 5468 113.72 - 120.48: 3791 120.48 - 127.23: 3275 127.23 - 133.99: 208 Bond angle restraints: 13391 Sorted by residual: angle pdb=" N ARG A 965 " pdb=" CA ARG A 965 " pdb=" C ARG A 965 " ideal model delta sigma weight residual 112.75 103.96 8.79 1.36e+00 5.41e-01 4.18e+01 angle pdb=" C PRO A 966 " pdb=" CA PRO A 966 " pdb=" CB PRO A 966 " ideal model delta sigma weight residual 112.64 105.72 6.92 1.74e+00 3.30e-01 1.58e+01 angle pdb=" CA ALA A 962 " pdb=" C ALA A 962 " pdb=" O ALA A 962 " ideal model delta sigma weight residual 120.90 117.03 3.87 1.03e+00 9.43e-01 1.41e+01 angle pdb=" CA GLY A1067 " pdb=" C GLY A1067 " pdb=" O GLY A1067 " ideal model delta sigma weight residual 120.80 117.50 3.30 9.80e-01 1.04e+00 1.13e+01 angle pdb=" CA THR A 967 " pdb=" C THR A 967 " pdb=" O THR A 967 " ideal model delta sigma weight residual 120.55 117.06 3.49 1.06e+00 8.90e-01 1.08e+01 ... (remaining 13386 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.00: 5582 30.00 - 60.00: 244 60.00 - 90.00: 66 90.00 - 120.00: 2 120.00 - 150.00: 1 Dihedral angle restraints: 5895 sinusoidal: 3037 harmonic: 2858 Sorted by residual: dihedral pdb=" O4' U B 19 " pdb=" C1' U B 19 " pdb=" N1 U B 19 " pdb=" C2 U B 19 " ideal model delta sinusoidal sigma weight residual 200.00 50.00 150.00 1 1.50e+01 4.44e-03 7.96e+01 dihedral pdb=" C8 GTP B 1 " pdb=" C1' GTP B 1 " pdb=" N9 GTP B 1 " pdb=" O4' GTP B 1 " ideal model delta sinusoidal sigma weight residual 104.59 6.23 98.37 1 2.00e+01 2.50e-03 2.75e+01 dihedral pdb=" O2G GTP B 1 " pdb=" O3B GTP B 1 " pdb=" PG GTP B 1 " pdb=" PB GTP B 1 " ideal model delta sinusoidal sigma weight residual 177.30 -86.23 -96.47 1 2.00e+01 2.50e-03 2.67e+01 ... (remaining 5892 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1220 0.043 - 0.087: 274 0.087 - 0.130: 72 0.130 - 0.174: 8 0.174 - 0.217: 3 Chirality restraints: 1577 Sorted by residual: chirality pdb=" CA SER A 964 " pdb=" N SER A 964 " pdb=" C SER A 964 " pdb=" CB SER A 964 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" C2' C B 2 " pdb=" C3' C B 2 " pdb=" O2' C B 2 " pdb=" C1' C B 2 " both_signs ideal model delta sigma weight residual False -2.75 -2.58 -0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" C3' GTP B 1 " pdb=" C2' GTP B 1 " pdb=" C4' GTP B 1 " pdb=" O3' GTP B 1 " both_signs ideal model delta sigma weight residual False -2.47 -2.65 0.17 2.00e-01 2.50e+01 7.56e-01 ... (remaining 1574 not shown) Planarity restraints: 1461 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 637 " -0.028 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO A 638 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 638 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 638 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A1063 " 0.008 2.00e-02 2.50e+03 1.56e-02 2.42e+00 pdb=" C SER A1063 " -0.027 2.00e-02 2.50e+03 pdb=" O SER A1063 " 0.010 2.00e-02 2.50e+03 pdb=" N VAL A1064 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 969 " 0.007 2.00e-02 2.50e+03 1.51e-02 2.29e+00 pdb=" C ILE A 969 " -0.026 2.00e-02 2.50e+03 pdb=" O ILE A 969 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE A 970 " 0.009 2.00e-02 2.50e+03 ... (remaining 1458 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1361 2.75 - 3.29: 8944 3.29 - 3.83: 15450 3.83 - 4.36: 17452 4.36 - 4.90: 28409 Nonbonded interactions: 71616 Sorted by model distance: nonbonded pdb=" O PHE A 950 " pdb=" OG1 THR A 953 " model vdw 2.218 2.440 nonbonded pdb=" OG1 THR A 855 " pdb=" OP1 G B 69 " model vdw 2.220 2.440 nonbonded pdb=" O GLU A 206 " pdb=" NH1 ARG A 234 " model vdw 2.241 2.520 nonbonded pdb=" OE1 GLU A 389 " pdb=" OH TYR A 584 " model vdw 2.244 2.440 nonbonded pdb=" OG1 THR A 255 " pdb=" OE1 GLU A 258 " model vdw 2.248 2.440 ... (remaining 71611 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.940 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 34.260 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.124 9614 Z= 0.230 Angle : 0.591 9.148 13391 Z= 0.321 Chirality : 0.040 0.217 1577 Planarity : 0.004 0.043 1461 Dihedral : 16.502 149.999 4047 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.13 % Allowed : 8.19 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.27), residues: 982 helix: -0.15 (0.26), residues: 439 sheet: -0.34 (0.52), residues: 119 loop : -1.59 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 194 HIS 0.004 0.001 HIS A 145 PHE 0.010 0.001 PHE A 544 TYR 0.012 0.001 TYR A 230 ARG 0.002 0.000 ARG A1045 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 92 time to evaluate : 0.936 Fit side-chains revert: symmetry clash REVERT: A 263 ASN cc_start: 0.7814 (t0) cc_final: 0.7556 (t0) REVERT: A 267 MET cc_start: 0.9033 (mmm) cc_final: 0.8695 (mmp) REVERT: A 495 TYR cc_start: 0.4079 (OUTLIER) cc_final: 0.2605 (m-80) REVERT: A 597 MET cc_start: 0.8677 (tmm) cc_final: 0.8469 (tmm) REVERT: A 653 ASP cc_start: 0.8157 (p0) cc_final: 0.7514 (t0) REVERT: A 714 MET cc_start: 0.8508 (tmm) cc_final: 0.8173 (tmm) REVERT: A 775 MET cc_start: 0.8274 (tmm) cc_final: 0.7898 (tmm) REVERT: A 793 MET cc_start: 0.8824 (mmm) cc_final: 0.8494 (mmm) REVERT: A 875 ASN cc_start: 0.8994 (OUTLIER) cc_final: 0.8726 (m-40) REVERT: A 963 TYR cc_start: 0.8811 (OUTLIER) cc_final: 0.7770 (t80) outliers start: 26 outliers final: 7 residues processed: 113 average time/residue: 0.2601 time to fit residues: 39.0489 Evaluate side-chains 62 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 52 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 963 TYR Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 1064 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 53 optimal weight: 0.0370 chunk 42 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 31 optimal weight: 0.0030 chunk 50 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 overall best weight: 0.8072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9614 Z= 0.144 Angle : 0.521 8.056 13391 Z= 0.260 Chirality : 0.039 0.143 1577 Planarity : 0.004 0.040 1461 Dihedral : 17.691 149.936 2215 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.53 % Allowed : 12.65 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.27), residues: 982 helix: 0.03 (0.26), residues: 440 sheet: -0.04 (0.55), residues: 105 loop : -1.56 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 542 HIS 0.003 0.001 HIS A 145 PHE 0.024 0.001 PHE A 260 TYR 0.011 0.001 TYR A 230 ARG 0.006 0.000 ARG A 927 *********************** 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 78 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 57 time to evaluate : 0.917 Fit side-chains revert: symmetry clash REVERT: A 237 MET cc_start: 0.8358 (ttt) cc_final: 0.7967 (ttt) REVERT: A 263 ASN cc_start: 0.7887 (t0) cc_final: 0.7632 (t0) REVERT: A 267 MET cc_start: 0.9081 (mmm) cc_final: 0.8728 (mmp) REVERT: A 495 TYR cc_start: 0.4061 (OUTLIER) cc_final: 0.2520 (m-80) REVERT: A 597 MET cc_start: 0.8631 (tmm) cc_final: 0.8404 (tmm) REVERT: A 653 ASP cc_start: 0.8112 (p0) cc_final: 0.7548 (t0) REVERT: A 714 MET cc_start: 0.8487 (tmm) cc_final: 0.8100 (tmm) REVERT: A 775 MET cc_start: 0.8229 (tmm) cc_final: 0.7968 (tmm) REVERT: A 875 ASN cc_start: 0.8965 (OUTLIER) cc_final: 0.8729 (m-40) REVERT: A 906 GLN cc_start: 0.8028 (tm-30) cc_final: 0.7753 (tm-30) REVERT: A 963 TYR cc_start: 0.8743 (OUTLIER) cc_final: 0.8026 (t80) outliers start: 21 outliers final: 10 residues processed: 75 average time/residue: 0.1908 time to fit residues: 21.2330 Evaluate side-chains 64 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 51 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 155 ASP 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 495 TYR Chi-restraints excluded: chain A residue 550 LEU 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 1029 PHE 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 52 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 GLN ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9614 Z= 0.176 Angle : 0.518 6.950 13391 Z= 0.258 Chirality : 0.039 0.171 1577 Planarity : 0.004 0.044 1461 Dihedral : 17.512 149.048 2213 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.53 % Allowed : 13.49 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.27), residues: 982 helix: 0.09 (0.26), residues: 440 sheet: -0.15 (0.54), residues: 107 loop : -1.57 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 542 HIS 0.007 0.001 HIS A 274 PHE 0.009 0.001 PHE A 544 TYR 0.015 0.001 TYR A 230 ARG 0.007 0.000 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 53 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: A 237 MET cc_start: 0.8376 (ttt) cc_final: 0.8064 (ttt) REVERT: A 263 ASN cc_start: 0.7964 (t0) cc_final: 0.7754 (t0) REVERT: A 267 MET cc_start: 0.9117 (mmm) cc_final: 0.8868 (mmp) REVERT: A 495 TYR cc_start: 0.3958 (OUTLIER) cc_final: 0.2400 (m-80) REVERT: A 597 MET cc_start: 0.8590 (tmm) cc_final: 0.8372 (tmm) REVERT: A 653 ASP cc_start: 0.8156 (p0) cc_final: 0.7598 (t0) REVERT: A 714 MET cc_start: 0.8479 (tmm) cc_final: 0.8087 (tmm) REVERT: A 875 ASN cc_start: 0.8990 (OUTLIER) cc_final: 0.8750 (m-40) REVERT: A 906 GLN cc_start: 0.7943 (tm-30) cc_final: 0.7177 (tm-30) REVERT: A 910 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7368 (tpp-160) REVERT: A 963 TYR cc_start: 0.8807 (OUTLIER) cc_final: 0.7922 (t80) REVERT: A 1052 VAL cc_start: 0.8239 (t) cc_final: 0.8034 (t) outliers start: 21 outliers final: 12 residues processed: 70 average time/residue: 0.1962 time to fit residues: 20.1118 Evaluate side-chains 64 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 48 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 910 ARG Chi-restraints excluded: chain A residue 963 TYR Chi-restraints excluded: chain A residue 1029 PHE 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 94 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9614 Z= 0.160 Angle : 0.539 16.732 13391 Z= 0.259 Chirality : 0.039 0.162 1577 Planarity : 0.004 0.042 1461 Dihedral : 17.442 148.922 2212 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.53 % Allowed : 13.25 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.27), residues: 982 helix: 0.10 (0.26), residues: 440 sheet: -0.33 (0.52), residues: 112 loop : -1.54 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 542 HIS 0.002 0.000 HIS A 145 PHE 0.008 0.001 PHE A 986 TYR 0.014 0.001 TYR A 230 ARG 0.007 0.000 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 50 time to evaluate : 0.997 Fit side-chains REVERT: A 237 MET cc_start: 0.8385 (ttt) cc_final: 0.8150 (ttt) REVERT: A 274 HIS cc_start: 0.8187 (OUTLIER) cc_final: 0.7528 (m170) REVERT: A 495 TYR cc_start: 0.3932 (OUTLIER) cc_final: 0.2361 (m-80) REVERT: A 597 MET cc_start: 0.8600 (tmm) cc_final: 0.8372 (tmm) REVERT: A 653 ASP cc_start: 0.8171 (p0) cc_final: 0.7604 (t0) REVERT: A 714 MET cc_start: 0.8474 (tmm) cc_final: 0.8167 (tmm) REVERT: A 743 MET cc_start: 0.8801 (mmt) cc_final: 0.8377 (mmm) REVERT: A 927 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.8373 (tpm170) REVERT: A 963 TYR cc_start: 0.8830 (OUTLIER) cc_final: 0.7953 (t80) REVERT: A 1052 VAL cc_start: 0.8248 (t) cc_final: 0.8041 (t) outliers start: 21 outliers final: 13 residues processed: 67 average time/residue: 0.2179 time to fit residues: 21.2741 Evaluate side-chains 61 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 44 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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 274 HIS Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 927 ARG Chi-restraints excluded: chain A residue 963 TYR Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1064 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 1.9990 chunk 57 optimal weight: 0.0470 chunk 1 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 overall best weight: 2.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 ASN ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9614 Z= 0.236 Angle : 0.568 11.525 13391 Z= 0.278 Chirality : 0.040 0.158 1577 Planarity : 0.004 0.049 1461 Dihedral : 17.528 147.466 2208 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.01 % Allowed : 13.86 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.27), residues: 982 helix: 0.01 (0.26), residues: 440 sheet: -0.49 (0.52), residues: 112 loop : -1.41 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 198 HIS 0.003 0.001 HIS A 662 PHE 0.012 0.001 PHE A 544 TYR 0.016 0.001 TYR A 230 ARG 0.007 0.000 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 45 time to evaluate : 0.963 Fit side-chains REVERT: A 495 TYR cc_start: 0.4603 (OUTLIER) cc_final: 0.2719 (m-80) REVERT: A 597 MET cc_start: 0.8712 (tmm) cc_final: 0.8480 (tmm) REVERT: A 927 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.8447 (tpm170) REVERT: A 963 TYR cc_start: 0.8930 (OUTLIER) cc_final: 0.8002 (t80) outliers start: 25 outliers final: 15 residues processed: 66 average time/residue: 0.2101 time to fit residues: 20.0540 Evaluate side-chains 60 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 42 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 155 ASP 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 330 ARG Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 927 ARG Chi-restraints excluded: chain A residue 963 TYR Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1064 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 0.0020 chunk 53 optimal weight: 0.9980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS A 263 ASN ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9614 Z= 0.131 Angle : 0.524 13.431 13391 Z= 0.252 Chirality : 0.038 0.161 1577 Planarity : 0.004 0.043 1461 Dihedral : 17.391 147.708 2208 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.53 % Allowed : 14.34 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.27), residues: 982 helix: 0.12 (0.26), residues: 440 sheet: -0.33 (0.52), residues: 110 loop : -1.39 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 530 HIS 0.002 0.000 HIS A 145 PHE 0.010 0.001 PHE A 986 TYR 0.010 0.001 TYR A 230 ARG 0.006 0.000 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 47 time to evaluate : 0.927 Fit side-chains REVERT: A 160 GLN cc_start: 0.8664 (pt0) cc_final: 0.8398 (pt0) REVERT: A 237 MET cc_start: 0.8368 (ttt) cc_final: 0.8054 (ttt) REVERT: A 274 HIS cc_start: 0.8342 (OUTLIER) cc_final: 0.7468 (m-70) REVERT: A 495 TYR cc_start: 0.4381 (OUTLIER) cc_final: 0.2580 (m-80) REVERT: A 597 MET cc_start: 0.8702 (tmm) cc_final: 0.8441 (tmm) REVERT: A 743 MET cc_start: 0.8870 (mmt) cc_final: 0.8394 (mmm) REVERT: A 927 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8316 (tpm170) REVERT: A 947 MET cc_start: 0.7759 (ttp) cc_final: 0.7437 (ttp) REVERT: A 963 TYR cc_start: 0.8945 (OUTLIER) cc_final: 0.7966 (t80) outliers start: 21 outliers final: 14 residues processed: 65 average time/residue: 0.2059 time to fit residues: 19.7837 Evaluate side-chains 61 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 43 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 274 HIS 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 550 LEU Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 927 ARG 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 97 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 57 optimal weight: 0.0020 chunk 74 optimal weight: 0.0040 chunk 85 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 46 optimal weight: 0.0870 chunk 62 optimal weight: 0.8980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN A 341 GLN ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9614 Z= 0.123 Angle : 0.520 13.797 13391 Z= 0.247 Chirality : 0.038 0.156 1577 Planarity : 0.004 0.039 1461 Dihedral : 17.319 148.515 2208 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.29 % Allowed : 15.06 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.27), residues: 982 helix: 0.22 (0.26), residues: 439 sheet: -0.21 (0.53), residues: 110 loop : -1.32 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 542 HIS 0.002 0.000 HIS A 145 PHE 0.010 0.001 PHE A 986 TYR 0.012 0.001 TYR A 212 ARG 0.004 0.000 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 50 time to evaluate : 0.960 Fit side-chains REVERT: A 160 GLN cc_start: 0.8625 (pt0) cc_final: 0.8348 (pt0) REVERT: A 274 HIS cc_start: 0.8232 (OUTLIER) cc_final: 0.7466 (m-70) REVERT: A 495 TYR cc_start: 0.4200 (OUTLIER) cc_final: 0.2399 (m-80) REVERT: A 597 MET cc_start: 0.8587 (tmm) cc_final: 0.8343 (tmm) REVERT: A 653 ASP cc_start: 0.8145 (p0) cc_final: 0.7617 (t0) REVERT: A 743 MET cc_start: 0.8859 (mmt) cc_final: 0.8396 (mmm) REVERT: A 927 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.8271 (tpm170) REVERT: A 963 TYR cc_start: 0.8923 (OUTLIER) cc_final: 0.8005 (t80) outliers start: 19 outliers final: 13 residues processed: 65 average time/residue: 0.1979 time to fit residues: 19.1708 Evaluate side-chains 65 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 48 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 274 HIS 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 550 LEU Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 927 ARG Chi-restraints excluded: chain A residue 963 TYR Chi-restraints excluded: chain A residue 1029 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 0.3980 chunk 60 optimal weight: 0.0970 chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 9 optimal weight: 0.2980 chunk 79 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9614 Z= 0.133 Angle : 0.526 12.128 13391 Z= 0.251 Chirality : 0.038 0.161 1577 Planarity : 0.004 0.040 1461 Dihedral : 17.292 149.000 2207 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.41 % Allowed : 15.54 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.27), residues: 982 helix: 0.29 (0.26), residues: 439 sheet: -0.17 (0.52), residues: 112 loop : -1.38 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 542 HIS 0.003 0.000 HIS A1006 PHE 0.010 0.001 PHE A 986 TYR 0.011 0.001 TYR A 212 ARG 0.004 0.000 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 46 time to evaluate : 0.975 Fit side-chains REVERT: A 160 GLN cc_start: 0.8618 (pt0) cc_final: 0.8343 (pt0) REVERT: A 274 HIS cc_start: 0.8248 (OUTLIER) cc_final: 0.7462 (m-70) REVERT: A 495 TYR cc_start: 0.4092 (OUTLIER) cc_final: 0.2396 (m-80) REVERT: A 597 MET cc_start: 0.8571 (tmm) cc_final: 0.8325 (tmm) REVERT: A 653 ASP cc_start: 0.8178 (p0) cc_final: 0.7673 (t0) REVERT: A 775 MET cc_start: 0.8433 (tmm) cc_final: 0.8044 (tmm) REVERT: A 927 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8252 (tpm170) REVERT: A 963 TYR cc_start: 0.8916 (OUTLIER) cc_final: 0.8006 (t80) outliers start: 20 outliers final: 14 residues processed: 62 average time/residue: 0.2015 time to fit residues: 18.5489 Evaluate side-chains 63 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 45 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 927 ARG Chi-restraints excluded: chain A residue 963 TYR Chi-restraints excluded: chain A residue 1029 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 41 optimal weight: 0.0370 chunk 74 optimal weight: 3.9990 chunk 28 optimal weight: 0.0040 chunk 85 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.5872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9614 Z= 0.123 Angle : 0.515 11.464 13391 Z= 0.246 Chirality : 0.038 0.150 1577 Planarity : 0.003 0.039 1461 Dihedral : 17.268 149.479 2207 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.05 % Allowed : 15.90 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.27), residues: 982 helix: 0.35 (0.26), residues: 439 sheet: -0.10 (0.52), residues: 112 loop : -1.38 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 542 HIS 0.002 0.000 HIS A 145 PHE 0.011 0.001 PHE A 986 TYR 0.011 0.001 TYR A 212 ARG 0.004 0.000 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 46 time to evaluate : 0.755 Fit side-chains REVERT: A 160 GLN cc_start: 0.8591 (pt0) cc_final: 0.8226 (pt0) REVERT: A 495 TYR cc_start: 0.3940 (OUTLIER) cc_final: 0.2291 (m-80) REVERT: A 597 MET cc_start: 0.8559 (tmm) cc_final: 0.8312 (tmm) REVERT: A 653 ASP cc_start: 0.8125 (p0) cc_final: 0.7644 (t0) REVERT: A 743 MET cc_start: 0.8810 (mmt) cc_final: 0.8474 (mmm) REVERT: A 775 MET cc_start: 0.8500 (tmm) cc_final: 0.8297 (tmm) REVERT: A 927 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.8253 (tpm170) REVERT: A 963 TYR cc_start: 0.8916 (OUTLIER) cc_final: 0.7969 (t80) REVERT: A 1052 VAL cc_start: 0.8134 (t) cc_final: 0.7909 (t) outliers start: 17 outliers final: 14 residues processed: 59 average time/residue: 0.2082 time to fit residues: 18.0184 Evaluate side-chains 62 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 45 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 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 550 LEU Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 927 ARG Chi-restraints excluded: chain A residue 963 TYR Chi-restraints excluded: chain A residue 1029 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 10.0000 chunk 60 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 83 optimal weight: 0.0060 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 0.0050 chunk 51 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.5210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9614 Z= 0.121 Angle : 0.510 11.410 13391 Z= 0.243 Chirality : 0.038 0.149 1577 Planarity : 0.003 0.038 1461 Dihedral : 17.245 149.823 2207 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.05 % Allowed : 15.66 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.27), residues: 982 helix: 0.46 (0.26), residues: 436 sheet: -0.07 (0.52), residues: 112 loop : -1.40 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 542 HIS 0.002 0.000 HIS A 145 PHE 0.010 0.001 PHE A 986 TYR 0.011 0.001 TYR A 212 ARG 0.003 0.000 ARG A 144 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 47 time to evaluate : 1.007 Fit side-chains REVERT: A 160 GLN cc_start: 0.8566 (pt0) cc_final: 0.8222 (pt0) REVERT: A 274 HIS cc_start: 0.8128 (OUTLIER) cc_final: 0.7380 (m-70) REVERT: A 495 TYR cc_start: 0.3838 (OUTLIER) cc_final: 0.2201 (m-80) REVERT: A 597 MET cc_start: 0.8550 (tmm) cc_final: 0.8302 (tmm) REVERT: A 653 ASP cc_start: 0.8104 (p0) cc_final: 0.7639 (t0) REVERT: A 743 MET cc_start: 0.8808 (mmt) cc_final: 0.8457 (mmm) REVERT: A 927 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8245 (tpm170) REVERT: A 963 TYR cc_start: 0.8923 (OUTLIER) cc_final: 0.8020 (t80) REVERT: A 1052 VAL cc_start: 0.8109 (t) cc_final: 0.7881 (t) outliers start: 17 outliers final: 12 residues processed: 61 average time/residue: 0.2169 time to fit residues: 19.7560 Evaluate side-chains 61 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 45 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 274 HIS 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 550 LEU Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 927 ARG Chi-restraints excluded: chain A residue 963 TYR Chi-restraints excluded: chain A residue 1029 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 83 optimal weight: 0.0870 chunk 34 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** 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 = 0.3609 r_free = 0.3609 target = 0.095014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.072065 restraints weight = 26504.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.073844 restraints weight = 14700.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.074906 restraints weight = 9778.942| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9614 Z= 0.240 Angle : 0.571 15.354 13391 Z= 0.275 Chirality : 0.040 0.141 1577 Planarity : 0.004 0.047 1461 Dihedral : 17.360 148.100 2207 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.29 % Allowed : 15.42 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.27), residues: 982 helix: 0.34 (0.26), residues: 440 sheet: -0.15 (0.54), residues: 110 loop : -1.39 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 198 HIS 0.003 0.001 HIS A 145 PHE 0.011 0.001 PHE A 544 TYR 0.017 0.001 TYR A 230 ARG 0.007 0.000 ARG A 144 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1782.26 seconds wall clock time: 32 minutes 53.80 seconds (1973.80 seconds total)