Starting phenix.real_space_refine on Wed Feb 14 11:59:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk0_33239/02_2024/7xk0_33239_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk0_33239/02_2024/7xk0_33239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk0_33239/02_2024/7xk0_33239.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk0_33239/02_2024/7xk0_33239.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk0_33239/02_2024/7xk0_33239_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk0_33239/02_2024/7xk0_33239_updated.pdb" } resolution = 3.59 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= -0.001 sd= 0.088 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 73 5.49 5 S 31 5.16 5 C 5581 2.51 5 N 1589 2.21 5 O 1934 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "A PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 181": "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 PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 258": "OE1" <-> "OE2" Residue "A ASP 278": "OD1" <-> "OD2" Residue "A PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 305": "OD1" <-> "OD2" Residue "A GLU 402": "OE1" <-> "OE2" Residue "A GLU 472": "OE1" <-> "OE2" Residue "A ASP 483": "OD1" <-> "OD2" Residue "A ARG 487": "NH1" <-> "NH2" Residue "A TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 579": "OE1" <-> "OE2" Residue "A GLU 628": "OE1" <-> "OE2" Residue "A TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 653": "OD1" <-> "OD2" Residue "A PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 715": "OD1" <-> "OD2" Residue "A ASP 769": "OD1" <-> "OD2" Residue "A PHE 819": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 857": "OD1" <-> "OD2" Residue "A TYR 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 897": "OD1" <-> "OD2" Residue "A ASP 902": "OD1" <-> "OD2" Residue "A GLU 903": "OE1" <-> "OE2" Residue "A ASP 955": "OD1" <-> "OD2" Residue "A ARG 965": "NH1" <-> "NH2" Residue "A PHE 986": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 991": "OE1" <-> "OE2" Residue "A ASP 1003": "OD1" <-> "OD2" Residue "A ASP 1010": "OD1" <-> "OD2" Residue "A GLU 1020": "OE1" <-> "OE2" Residue "A GLU 1026": "OE1" <-> "OE2" Residue "A ASP 1027": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9208 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7688 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 983, 7683 Classifications: {'peptide': 983} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 3, 'PTRANS': 43, 'TRANS': 936} Chain breaks: 1 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 10, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 71 Conformer: "B" Number of residues, atoms: 983, 7683 Classifications: {'peptide': 983} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 3, 'PTRANS': 43, 'TRANS': 936} Chain breaks: 1 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 10, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 71 bond proxies already assigned to first conformer: 7834 Chain: "B" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1520 Unusual residues: {'GTP': 1} Classifications: {'RNA': 70, 'undetermined': 1} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 5, 'rna3p_pur': 31, 'rna3p_pyr': 30} Link IDs: {'rna2p': 9, 'rna3p': 60, None: 1} Not linked: pdbres="GTP B 1 " pdbres=" C B 2 " Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AALA A 940 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA A 940 " occ=0.50 Time building chain proxies: 9.12, per 1000 atoms: 0.99 Number of scatterers: 9208 At special positions: 0 Unit cell: (126.5, 106.7, 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 73 15.00 O 1934 8.00 N 1589 7.00 C 5581 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: 4.29 Conformation dependent library (CDL) restraints added in 2.8 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: 40 helices and 7 sheets defined 36.8% alpha, 7.0% beta 17 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 4.17 Creating SS restraints... Processing helix chain 'A' and resid 74 through 88 removed outlier: 3.899A pdb=" N ILE A 78 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASP A 83 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA A 86 " --> pdb=" O GLN A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 110 No H-bonds generated for 'chain 'A' and resid 107 through 110' 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 163 through 169 removed outlier: 3.629A pdb=" N SER A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 247 No H-bonds generated for 'chain 'A' and resid 245 through 247' Processing helix chain 'A' and resid 257 through 272 removed outlier: 7.199A pdb=" N GLU A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASN A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER A 268 " --> pdb=" O GLU A 264 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR A 270 " --> pdb=" O GLU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 293 removed outlier: 3.868A pdb=" N ASP A 285 " --> pdb=" O GLN A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 318 removed outlier: 4.216A pdb=" N VAL A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 316 " --> pdb=" O HIS A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 351 removed outlier: 3.656A pdb=" N GLY A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER A 337 " --> pdb=" O GLY A 333 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU A 338 " --> pdb=" O ARG A 334 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA A 339 " --> pdb=" O MET A 335 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN A 341 " --> pdb=" O SER A 337 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLN A 344 " --> pdb=" O ARG A 340 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS A 348 " --> pdb=" O GLN A 344 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 417 removed outlier: 3.949A pdb=" N ILE A 414 " --> pdb=" O SER A 410 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU A 416 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 476 Processing helix chain 'A' and resid 511 through 521 Proline residue: A 516 - end of helix removed outlier: 3.646A pdb=" N GLY A 521 " --> pdb=" O THR A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 590 removed outlier: 3.650A pdb=" N LYS A 590 " --> pdb=" O HIS A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 604 removed outlier: 4.260A pdb=" N LYS A 601 " --> pdb=" O GLN A 598 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLN A 602 " --> pdb=" O GLU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 615 removed outlier: 3.536A pdb=" N VAL A 615 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 632 removed outlier: 4.516A pdb=" N ASN A 631 " --> pdb=" O GLN A 627 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU A 632 " --> pdb=" O GLU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 647 No H-bonds generated for 'chain 'A' and resid 645 through 647' Processing helix chain 'A' and resid 652 through 661 removed outlier: 4.193A pdb=" N THR A 657 " --> pdb=" O ASP A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 697 Processing helix chain 'A' and resid 704 through 715 removed outlier: 3.727A pdb=" N PHE A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 722 No H-bonds generated for 'chain 'A' and resid 720 through 722' Processing helix chain 'A' and resid 727 through 729 No H-bonds generated for 'chain 'A' and resid 727 through 729' Processing helix chain 'A' and resid 740 through 747 removed outlier: 3.790A pdb=" N GLU A 747 " --> pdb=" O MET A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 756 No H-bonds generated for 'chain 'A' and resid 753 through 756' Processing helix chain 'A' and resid 761 through 772 Proline residue: A 765 - end of helix removed outlier: 4.932A pdb=" N ASP A 769 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA A 772 " --> pdb=" O ASP A 769 " (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 781 through 785 removed outlier: 3.611A pdb=" N GLU A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 781 through 785' Processing helix chain 'A' and resid 792 through 801 removed outlier: 4.474A pdb=" N TYR A 797 " --> pdb=" O MET A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 810 Processing helix chain 'A' and resid 828 through 846 removed outlier: 4.096A pdb=" N VAL A 832 " --> pdb=" O ASP A 828 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU A 833 " --> pdb=" O PRO A 829 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA A 834 " --> pdb=" O GLY A 830 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG A 838 " --> pdb=" O ALA A 834 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A 845 " --> pdb=" O SER A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 873 removed outlier: 3.809A pdb=" N LEU A 868 " --> pdb=" O ILE A 864 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL A 869 " --> pdb=" O SER A 865 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN A 870 " --> pdb=" O TYR A 866 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 884 No H-bonds generated for 'chain 'A' and resid 881 through 884' Processing helix chain 'A' and resid 901 through 919 removed outlier: 3.587A pdb=" N VAL A 905 " --> pdb=" O ILE A 901 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLN A 906 " --> pdb=" O ASP A 902 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG A 911 " --> pdb=" O PHE A 907 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP A 918 " --> pdb=" O GLN A 914 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLU A 919 " --> pdb=" O LEU A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 951 removed outlier: 3.666A pdb=" N SER A 941 " --> pdb=" O PRO A 937 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE A 945 " --> pdb=" O SER A 941 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET A 947 " --> pdb=" O THR A 943 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU A 948 " --> pdb=" O ALA A 944 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA A 949 " --> pdb=" O ILE A 945 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE A 950 " --> pdb=" O GLU A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 962 removed outlier: 3.682A pdb=" N GLU A 961 " --> pdb=" O PRO A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 968 No H-bonds generated for 'chain 'A' and resid 965 through 968' Processing helix chain 'A' and resid 991 through 1002 removed outlier: 4.417A pdb=" N SER A 996 " --> pdb=" O ARG A 992 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA A 997 " --> pdb=" O ALA A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1017 Processing helix chain 'A' and resid 1021 through 1028 removed outlier: 3.595A pdb=" N LEU A1025 " --> pdb=" O LEU A1021 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU A1026 " --> pdb=" O LEU A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1054 removed outlier: 4.189A pdb=" N LEU A1049 " --> pdb=" O ARG A1045 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL A1052 " --> pdb=" O LEU A1048 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 121 through 123 removed outlier: 3.614A pdb=" N GLN A 209 " --> pdb=" O THR A 229 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR A 208 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N TRP A 194 " --> pdb=" O GLN A 214 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 126 through 128 Processing sheet with id= C, first strand: chain 'A' and resid 186 through 188 Processing sheet with id= D, first strand: chain 'A' and resid 543 through 547 Processing sheet with id= E, first strand: chain 'A' and resid 451 through 453 removed outlier: 3.575A pdb=" N LEU A 452 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A 498 " --> pdb=" O LEU A 452 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 617 through 619 Processing sheet with id= G, first strand: chain 'A' and resid 636 through 641 removed outlier: 3.776A pdb=" N MET A 637 " --> pdb=" O ALA A 684 " (cutoff:3.500A) 184 hydrogen bonds defined for protein. 510 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 3.73 Time building geometry restraints manager: 4.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1395 1.31 - 1.43: 2870 1.43 - 1.56: 5080 1.56 - 1.68: 145 1.68 - 1.81: 52 Bond restraints: 9542 Sorted by residual: bond pdb=" C8 GTP B 1 " pdb=" N9 GTP B 1 " ideal model delta sigma weight residual 1.370 1.197 0.173 2.00e-02 2.50e+03 7.44e+01 bond pdb=" C4 GTP B 1 " pdb=" N9 GTP B 1 " ideal model delta sigma weight residual 1.375 1.214 0.161 2.00e-02 2.50e+03 6.51e+01 bond pdb=" O2G GTP B 1 " pdb=" PG GTP B 1 " ideal model delta sigma weight residual 1.510 1.649 -0.139 2.00e-02 2.50e+03 4.81e+01 bond pdb=" C2 GTP B 1 " pdb=" N2 GTP B 1 " ideal model delta sigma weight residual 1.330 1.450 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" C1' GTP B 1 " pdb=" O4' GTP B 1 " ideal model delta sigma weight residual 1.410 1.508 -0.098 2.00e-02 2.50e+03 2.41e+01 ... (remaining 9537 not shown) Histogram of bond angle deviations from ideal: 99.41 - 106.96: 655 106.96 - 114.51: 5693 114.51 - 122.06: 5214 122.06 - 129.61: 1637 129.61 - 137.16: 89 Bond angle restraints: 13288 Sorted by residual: angle pdb=" N GLY A 737 " pdb=" CA GLY A 737 " pdb=" C GLY A 737 " ideal model delta sigma weight residual 111.56 119.92 -8.36 1.01e+00 9.80e-01 6.85e+01 angle pdb=" C4 GTP B 1 " pdb=" N9 GTP B 1 " pdb=" C8 GTP B 1 " ideal model delta sigma weight residual 108.00 122.32 -14.32 3.00e+00 1.11e-01 2.28e+01 angle pdb=" CA ARG A 965 " pdb=" C ARG A 965 " pdb=" N PRO A 966 " ideal model delta sigma weight residual 118.44 125.95 -7.51 1.59e+00 3.96e-01 2.23e+01 angle pdb=" C ARG A 529 " pdb=" N TRP A 530 " pdb=" CA TRP A 530 " ideal model delta sigma weight residual 122.58 113.93 8.65 2.07e+00 2.33e-01 1.75e+01 angle pdb=" N ILE A 945 " pdb=" CA ILE A 945 " pdb=" C ILE A 945 " ideal model delta sigma weight residual 111.00 106.83 4.17 1.09e+00 8.42e-01 1.46e+01 ... (remaining 13283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.70: 5550 35.70 - 71.39: 255 71.39 - 107.09: 32 107.09 - 142.78: 3 142.78 - 178.48: 2 Dihedral angle restraints: 5842 sinusoidal: 2984 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 232.00 60.17 171.83 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" O5' GTP B 1 " pdb=" O3A GTP B 1 " pdb=" PA GTP B 1 " pdb=" PB GTP B 1 " ideal model delta sinusoidal sigma weight residual 274.12 95.64 178.48 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C4' GTP B 1 " pdb=" C5' GTP B 1 " pdb=" O5' GTP B 1 " pdb=" PA GTP B 1 " ideal model delta sinusoidal sigma weight residual 260.87 139.34 121.54 1 2.00e+01 2.50e-03 3.66e+01 ... (remaining 5839 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1162 0.060 - 0.120: 351 0.120 - 0.180: 46 0.180 - 0.240: 4 0.240 - 0.300: 1 Chirality restraints: 1564 Sorted by residual: chirality pdb=" CB ILE A 970 " pdb=" CA ILE A 970 " pdb=" CG1 ILE A 970 " pdb=" CG2 ILE A 970 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" C1' U B 57 " pdb=" O4' U B 57 " pdb=" C2' U B 57 " pdb=" N1 U B 57 " both_signs ideal model delta sigma weight residual False 2.47 2.24 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA ARG A 965 " pdb=" N ARG A 965 " pdb=" C ARG A 965 " pdb=" CB ARG A 965 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1561 not shown) Planarity restraints: 1455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 637 " -0.047 5.00e-02 4.00e+02 7.05e-02 7.94e+00 pdb=" N PRO A 638 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO A 638 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 638 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 962 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.48e+00 pdb=" C ALA A 962 " 0.040 2.00e-02 2.50e+03 pdb=" O ALA A 962 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR A 963 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 57 " -0.028 2.00e-02 2.50e+03 1.54e-02 5.32e+00 pdb=" N1 U B 57 " 0.035 2.00e-02 2.50e+03 pdb=" C2 U B 57 " -0.000 2.00e-02 2.50e+03 pdb=" O2 U B 57 " 0.003 2.00e-02 2.50e+03 pdb=" N3 U B 57 " -0.002 2.00e-02 2.50e+03 pdb=" C4 U B 57 " -0.005 2.00e-02 2.50e+03 pdb=" O4 U B 57 " -0.006 2.00e-02 2.50e+03 pdb=" C5 U B 57 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U B 57 " 0.006 2.00e-02 2.50e+03 ... (remaining 1452 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1536 2.75 - 3.28: 8646 3.28 - 3.82: 14812 3.82 - 4.36: 17592 4.36 - 4.90: 28808 Nonbonded interactions: 71394 Sorted by model distance: nonbonded pdb=" O LYS A1040 " pdb=" ND2 ASN A1043 " model vdw 2.206 2.520 nonbonded pdb=" NH1 ARG A 724 " pdb=" O ALA A 772 " model vdw 2.210 2.520 nonbonded pdb=" O VAL A1041 " pdb=" NH1 ARG A1045 " model vdw 2.230 2.520 nonbonded pdb=" OE2 GLU A 233 " pdb=" OH TYR A 256 " model vdw 2.237 2.440 nonbonded pdb=" O PRO A 481 " pdb=" OG SER A 484 " model vdw 2.246 2.440 ... (remaining 71389 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.000 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 36.680 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: 0.010 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 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 : 0.011 0.173 9542 Z= 0.687 Angle : 0.958 14.317 13288 Z= 0.532 Chirality : 0.055 0.300 1564 Planarity : 0.006 0.070 1455 Dihedral : 19.034 178.481 3994 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer: Outliers : 5.36 % Allowed : 19.85 % Favored : 74.79 % 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: -5.27 (0.20), residues: 982 helix: -3.73 (0.17), residues: 421 sheet: -2.22 (0.51), residues: 98 loop : -3.52 (0.23), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 298 HIS 0.005 0.002 HIS A 586 PHE 0.024 0.002 PHE A1014 TYR 0.019 0.003 TYR A 584 ARG 0.006 0.001 ARG A 432 *********************** 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 103 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 59 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: A 264 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: A 486 TYR cc_start: 0.7549 (p90) cc_final: 0.6956 (p90) REVERT: A 739 MET cc_start: 0.8116 (mmm) cc_final: 0.7797 (mmt) REVERT: A 743 MET cc_start: 0.8116 (mmm) cc_final: 0.7620 (mmm) outliers start: 44 outliers final: 22 residues processed: 98 average time/residue: 0.2218 time to fit residues: 30.8014 Evaluate side-chains 68 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 45 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 936 CYS Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1063 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 31 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 94 GLN ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 HIS A 147 GLN ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 GLN A 249 GLN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 ASN A 598 GLN A 781 ASN A 856 ASN A1031 ASN A1043 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9542 Z= 0.294 Angle : 0.653 7.867 13288 Z= 0.331 Chirality : 0.045 0.182 1564 Planarity : 0.005 0.056 1455 Dihedral : 18.670 164.000 2205 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.35 % Favored : 92.54 % Rotamer: Outliers : 3.78 % Allowed : 21.07 % Favored : 75.15 % 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: -4.18 (0.23), residues: 982 helix: -2.86 (0.21), residues: 417 sheet: -1.80 (0.51), residues: 103 loop : -2.87 (0.25), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 995 HIS 0.003 0.001 HIS A 244 PHE 0.029 0.002 PHE A 322 TYR 0.017 0.002 TYR A 643 ARG 0.006 0.000 ARG A 292 *********************** 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 79 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 48 time to evaluate : 0.854 Fit side-chains revert: symmetry clash REVERT: A 159 SER cc_start: 0.9021 (OUTLIER) cc_final: 0.8798 (t) REVERT: A 214 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8232 (mt0) REVERT: A 264 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6317 (mp0) REVERT: A 486 TYR cc_start: 0.7606 (p90) cc_final: 0.7192 (p90) REVERT: A 743 MET cc_start: 0.8434 (mmm) cc_final: 0.7684 (mmt) REVERT: A 747 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7715 (pm20) REVERT: A 961 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.8042 (tm-30) outliers start: 31 outliers final: 21 residues processed: 77 average time/residue: 0.1739 time to fit residues: 20.5328 Evaluate side-chains 68 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 42 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 442 ASN Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 729 SER Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 936 CYS Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1050 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 0.0040 chunk 79 optimal weight: 3.9990 chunk 64 optimal weight: 0.0070 chunk 26 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 85 optimal weight: 0.5980 chunk 94 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 overall best weight: 0.4810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN A 214 GLN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9542 Z= 0.133 Angle : 0.541 9.368 13288 Z= 0.270 Chirality : 0.040 0.179 1564 Planarity : 0.004 0.048 1455 Dihedral : 18.131 175.268 2195 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.92 % Allowed : 22.29 % Favored : 74.79 % 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: -3.11 (0.25), residues: 982 helix: -2.07 (0.24), residues: 415 sheet: -1.43 (0.51), residues: 101 loop : -2.13 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 995 HIS 0.005 0.001 HIS A 145 PHE 0.023 0.001 PHE A 322 TYR 0.010 0.001 TYR A 84 ARG 0.005 0.000 ARG A 292 *********************** 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: 24 poor density : 50 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 252 LYS cc_start: 0.8947 (tmmm) cc_final: 0.8602 (ttpp) REVERT: A 264 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6427 (mp0) REVERT: A 267 MET cc_start: 0.8630 (tpp) cc_final: 0.8328 (tpt) REVERT: A 743 MET cc_start: 0.8257 (mmm) cc_final: 0.6987 (mmm) REVERT: A 846 PHE cc_start: 0.9086 (OUTLIER) cc_final: 0.8853 (t80) outliers start: 24 outliers final: 13 residues processed: 72 average time/residue: 0.1967 time to fit residues: 21.1954 Evaluate side-chains 58 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 43 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1029 PHE 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: 2.9990 chunk 49 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 95 optimal weight: 0.8980 chunk 101 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9542 Z= 0.237 Angle : 0.584 7.618 13288 Z= 0.291 Chirality : 0.043 0.157 1564 Planarity : 0.004 0.046 1455 Dihedral : 17.984 170.722 2184 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 3.17 % Allowed : 22.90 % Favored : 73.93 % 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: -2.87 (0.26), residues: 982 helix: -1.90 (0.24), residues: 414 sheet: -1.29 (0.52), residues: 102 loop : -1.96 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 194 HIS 0.004 0.001 HIS A 145 PHE 0.020 0.001 PHE A 322 TYR 0.016 0.001 TYR A 643 ARG 0.004 0.000 ARG A 292 *********************** 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 69 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 43 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: A 159 SER cc_start: 0.9024 (OUTLIER) cc_final: 0.8774 (t) REVERT: A 252 LYS cc_start: 0.8983 (tmmm) cc_final: 0.8610 (ttpp) REVERT: A 264 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6342 (mp0) REVERT: A 267 MET cc_start: 0.8628 (tpp) cc_final: 0.8360 (tpt) REVERT: A 743 MET cc_start: 0.8053 (mmm) cc_final: 0.7780 (mmm) outliers start: 26 outliers final: 15 residues processed: 67 average time/residue: 0.1651 time to fit residues: 17.2527 Evaluate side-chains 59 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 42 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 964 SER Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1025 LEU Chi-restraints excluded: chain A residue 1029 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 0.3980 chunk 57 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 GLN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 ASN A 547 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9542 Z= 0.207 Angle : 0.560 7.649 13288 Z= 0.279 Chirality : 0.042 0.160 1564 Planarity : 0.004 0.045 1455 Dihedral : 17.935 170.579 2184 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.05 % Allowed : 23.63 % Favored : 73.33 % 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: -2.56 (0.26), residues: 982 helix: -1.56 (0.25), residues: 406 sheet: -1.05 (0.52), residues: 101 loop : -1.90 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 194 HIS 0.004 0.001 HIS A 145 PHE 0.020 0.001 PHE A 322 TYR 0.014 0.001 TYR A 643 ARG 0.005 0.000 ARG A 292 *********************** 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 69 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 44 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 252 LYS cc_start: 0.8969 (tmmm) cc_final: 0.8575 (ttpp) REVERT: A 264 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6295 (mp0) REVERT: A 267 MET cc_start: 0.8579 (tpp) cc_final: 0.8321 (tpt) REVERT: A 461 PHE cc_start: 0.7357 (t80) cc_final: 0.7029 (t80) REVERT: A 743 MET cc_start: 0.8170 (mmm) cc_final: 0.7572 (mmm) REVERT: A 963 TYR cc_start: 0.8481 (m-10) cc_final: 0.8080 (m-10) outliers start: 25 outliers final: 17 residues processed: 66 average time/residue: 0.1625 time to fit residues: 17.4155 Evaluate side-chains 60 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 42 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1068 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 84 optimal weight: 0.6980 chunk 47 optimal weight: 0.0270 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 ASN A 547 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9542 Z= 0.136 Angle : 0.513 7.693 13288 Z= 0.253 Chirality : 0.040 0.145 1564 Planarity : 0.004 0.042 1455 Dihedral : 17.813 179.925 2183 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.44 % Allowed : 24.24 % Favored : 73.33 % 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: -2.23 (0.26), residues: 982 helix: -1.27 (0.26), residues: 407 sheet: -0.91 (0.53), residues: 101 loop : -1.72 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 194 HIS 0.004 0.001 HIS A 145 PHE 0.021 0.001 PHE A 322 TYR 0.012 0.001 TYR A 486 ARG 0.008 0.000 ARG A 965 *********************** 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: 20 poor density : 48 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8401 (mtt180) REVERT: A 252 LYS cc_start: 0.8925 (tmmm) cc_final: 0.8543 (ttpp) REVERT: A 267 MET cc_start: 0.8591 (tpp) cc_final: 0.8383 (tpt) REVERT: A 963 TYR cc_start: 0.8515 (m-10) cc_final: 0.8135 (m-10) outliers start: 20 outliers final: 14 residues processed: 64 average time/residue: 0.1912 time to fit residues: 18.8460 Evaluate side-chains 59 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 44 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1068 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 57 optimal weight: 0.0670 chunk 74 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 101 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 GLN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9542 Z= 0.137 Angle : 0.515 7.771 13288 Z= 0.253 Chirality : 0.040 0.156 1564 Planarity : 0.003 0.041 1455 Dihedral : 17.725 179.723 2180 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.44 % Allowed : 24.48 % Favored : 73.08 % 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: -2.02 (0.27), residues: 982 helix: -1.04 (0.26), residues: 408 sheet: -0.84 (0.53), residues: 101 loop : -1.66 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 194 HIS 0.005 0.001 HIS A 145 PHE 0.020 0.001 PHE A 322 TYR 0.009 0.001 TYR A 643 ARG 0.004 0.000 ARG A 292 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 47 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: A 252 LYS cc_start: 0.8921 (tmmm) cc_final: 0.8534 (ttpp) REVERT: A 264 GLU cc_start: 0.8082 (tp30) cc_final: 0.7275 (mm-30) REVERT: A 461 PHE cc_start: 0.7540 (t80) cc_final: 0.7134 (t80) REVERT: A 963 TYR cc_start: 0.8500 (m-10) cc_final: 0.8178 (m-10) outliers start: 20 outliers final: 15 residues processed: 64 average time/residue: 0.1624 time to fit residues: 16.6661 Evaluate side-chains 61 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 46 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 936 CYS Chi-restraints excluded: chain A residue 969 ILE 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: 10.0000 chunk 60 optimal weight: 0.0670 chunk 30 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 overall best weight: 1.3722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 HIS ** A 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9542 Z= 0.198 Angle : 0.549 7.878 13288 Z= 0.271 Chirality : 0.042 0.145 1564 Planarity : 0.004 0.043 1455 Dihedral : 17.709 173.737 2180 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.31 % Allowed : 24.85 % Favored : 72.84 % 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: -1.98 (0.27), residues: 982 helix: -1.02 (0.26), residues: 407 sheet: -0.75 (0.54), residues: 101 loop : -1.64 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 194 HIS 0.004 0.001 HIS A 145 PHE 0.021 0.001 PHE A 322 TYR 0.019 0.001 TYR A 486 ARG 0.004 0.000 ARG A 292 *********************** 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 64 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 45 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 252 LYS cc_start: 0.8953 (tmmm) cc_final: 0.8538 (ttpp) REVERT: A 461 PHE cc_start: 0.7567 (t80) cc_final: 0.7174 (t80) outliers start: 19 outliers final: 14 residues processed: 63 average time/residue: 0.1805 time to fit residues: 17.6379 Evaluate side-chains 58 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 44 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 936 CYS Chi-restraints excluded: chain A residue 969 ILE 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: 0.9980 chunk 94 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 28 optimal weight: 0.1980 chunk 85 optimal weight: 2.9990 chunk 89 optimal weight: 20.0000 chunk 93 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 HIS ** A 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9542 Z= 0.133 Angle : 0.511 7.891 13288 Z= 0.251 Chirality : 0.040 0.153 1564 Planarity : 0.003 0.042 1455 Dihedral : 17.666 178.924 2178 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.95 % Allowed : 25.33 % Favored : 72.72 % 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: -1.81 (0.27), residues: 982 helix: -0.81 (0.27), residues: 406 sheet: -0.71 (0.54), residues: 101 loop : -1.60 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 194 HIS 0.004 0.001 HIS A 145 PHE 0.021 0.001 PHE A 322 TYR 0.009 0.001 TYR A 643 ARG 0.003 0.000 ARG A 292 *********************** 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 64 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 48 time to evaluate : 1.026 Fit side-chains revert: symmetry clash REVERT: A 252 LYS cc_start: 0.8917 (tmmm) cc_final: 0.8520 (ttpp) REVERT: A 461 PHE cc_start: 0.7612 (t80) cc_final: 0.7337 (t80) REVERT: A 486 TYR cc_start: 0.6977 (p90) cc_final: 0.6312 (p90) outliers start: 16 outliers final: 15 residues processed: 63 average time/residue: 0.1888 time to fit residues: 18.4438 Evaluate side-chains 60 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 45 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 936 CYS Chi-restraints excluded: chain A residue 969 ILE 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: 9.9990 chunk 60 optimal weight: 0.8980 chunk 47 optimal weight: 0.0020 chunk 69 optimal weight: 0.0170 chunk 104 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 66 optimal weight: 0.0050 overall best weight: 0.3240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 HIS ** A 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9542 Z= 0.117 Angle : 0.494 7.871 13288 Z= 0.241 Chirality : 0.039 0.144 1564 Planarity : 0.003 0.043 1455 Dihedral : 17.628 179.217 2178 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.71 % Allowed : 26.07 % Favored : 72.23 % 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: -1.64 (0.27), residues: 982 helix: -0.57 (0.27), residues: 406 sheet: -1.19 (0.49), residues: 113 loop : -1.46 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 194 HIS 0.004 0.001 HIS A 145 PHE 0.021 0.001 PHE A 322 TYR 0.009 0.001 TYR A 84 ARG 0.003 0.000 ARG A 292 ********************** 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: 14 poor density : 50 time to evaluate : 0.917 Fit side-chains REVERT: A 252 LYS cc_start: 0.8924 (tmmm) cc_final: 0.8514 (ttpp) REVERT: A 461 PHE cc_start: 0.7780 (t80) cc_final: 0.7368 (t80) REVERT: A 486 TYR cc_start: 0.7033 (p90) cc_final: 0.6372 (p90) outliers start: 14 outliers final: 13 residues processed: 63 average time/residue: 0.1965 time to fit residues: 18.4233 Evaluate side-chains 58 residues out of total 848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 45 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 846 PHE Chi-restraints excluded: chain A residue 936 CYS Chi-restraints excluded: chain A residue 969 ILE 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: 0.9980 chunk 23 optimal weight: 0.0670 chunk 83 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 HIS A 748 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.108914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.085053 restraints weight = 17804.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.086620 restraints weight = 11589.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.087683 restraints weight = 8560.048| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9542 Z= 0.157 Angle : 0.530 9.219 13288 Z= 0.257 Chirality : 0.040 0.150 1564 Planarity : 0.003 0.040 1455 Dihedral : 17.630 176.756 2176 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.58 % Allowed : 26.55 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.27), residues: 982 helix: -0.55 (0.27), residues: 409 sheet: -0.69 (0.53), residues: 101 loop : -1.55 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 194 HIS 0.004 0.001 HIS A 145 PHE 0.021 0.001 PHE A 322 TYR 0.011 0.001 TYR A 230 ARG 0.004 0.000 ARG A 911 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1825.68 seconds wall clock time: 33 minutes 47.00 seconds (2027.00 seconds total)