Starting phenix.real_space_refine on Sat Nov 16 00:52:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bwt_44979/11_2024/9bwt_44979_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bwt_44979/11_2024/9bwt_44979.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bwt_44979/11_2024/9bwt_44979.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bwt_44979/11_2024/9bwt_44979.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bwt_44979/11_2024/9bwt_44979_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bwt_44979/11_2024/9bwt_44979_trim.cif" } resolution = 2.5 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= 0.058 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: 6 Type Number sf(0) Gaussians P 9 5.49 5 S 55 5.16 5 Cl 1 4.86 5 C 6402 2.51 5 N 1698 2.21 5 O 1790 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 9955 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 898, 6891 Classifications: {'peptide': 898} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 41, 'TRANS': 856} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 176 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 5, 'TPO:plan-1': 2, 'ASP:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 88 Chain: "B" Number of atoms: 2979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2979 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 17, 'TRANS': 355} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {'ATP': 1, 'HCZ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 6.43, per 1000 atoms: 0.65 Number of scatterers: 9955 At special positions: 0 Unit cell: (143.55, 99.825, 111.375, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 55 16.00 P 9 15.00 O 1790 8.00 N 1698 7.00 C 6402 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 415 " - pdb=" SG CYS A 420 " distance=2.03 Simple disulfide: pdb=" SG CYS A 429 " - pdb=" SG CYS A 435 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.87 Conformation dependent library (CDL) restraints added in 1.5 seconds 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2350 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 2 sheets defined 59.1% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 66 through 70 Processing helix chain 'A' and resid 85 through 90 Processing helix chain 'A' and resid 136 through 141 Processing helix chain 'A' and resid 141 through 150 Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 157 through 192 removed outlier: 6.760A pdb=" N ILE A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 9.178A pdb=" N VAL A 168 " --> pdb=" O GLN A 164 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU A 169 " --> pdb=" O ALA A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 211 Processing helix chain 'A' and resid 211 through 248 removed outlier: 3.844A pdb=" N SER A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 276 removed outlier: 3.772A pdb=" N ILE A 259 " --> pdb=" O PRO A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 303 Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 320 through 327 Processing helix chain 'A' and resid 338 through 347 Processing helix chain 'A' and resid 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'A' and resid 356 through 363 removed outlier: 3.592A pdb=" N ILE A 359 " --> pdb=" O GLY A 356 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A 360 " --> pdb=" O ALA A 357 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N GLY A 361 " --> pdb=" O ASN A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 394 Proline residue: A 371 - end of helix Processing helix chain 'A' and resid 403 through 407 removed outlier: 4.081A pdb=" N THR A 407 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 421 Processing helix chain 'A' and resid 426 through 433 Processing helix chain 'A' and resid 444 through 450 Processing helix chain 'A' and resid 452 through 486 removed outlier: 3.597A pdb=" N ILE A 456 " --> pdb=" O PHE A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 494 Processing helix chain 'A' and resid 504 through 522 removed outlier: 3.754A pdb=" N ILE A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 522 " --> pdb=" O PHE A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 553 Processing helix chain 'A' and resid 565 through 606 removed outlier: 3.694A pdb=" N THR A 584 " --> pdb=" O MET A 580 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N TRP A 586 " --> pdb=" O LEU A 582 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ALA A 587 " --> pdb=" O LEU A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 633 Processing helix chain 'A' and resid 636 through 640 removed outlier: 4.154A pdb=" N ASN A 639 " --> pdb=" O HIS A 636 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR A 640 " --> pdb=" O ILE A 637 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 636 through 640' Processing helix chain 'A' and resid 654 through 666 removed outlier: 3.794A pdb=" N VAL A 658 " --> pdb=" O ARG A 654 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE A 664 " --> pdb=" O PHE A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 702 Processing helix chain 'A' and resid 715 through 727 Processing helix chain 'A' and resid 749 through 766 removed outlier: 3.786A pdb=" N VAL A 753 " --> pdb=" O HIS A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 823 Processing helix chain 'A' and resid 840 through 850 Proline residue: A 846 - end of helix Processing helix chain 'A' and resid 875 through 885 removed outlier: 3.558A pdb=" N ILE A 879 " --> pdb=" O ARG A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 915 Processing helix chain 'A' and resid 916 through 918 No H-bonds generated for 'chain 'A' and resid 916 through 918' Processing helix chain 'A' and resid 925 through 934 removed outlier: 4.310A pdb=" N ASN A 930 " --> pdb=" O GLU A 926 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N GLU A 931 " --> pdb=" O ALA A 927 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N MET A 932 " --> pdb=" O THR A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 948 Processing helix chain 'A' and resid 949 through 966 removed outlier: 3.726A pdb=" N GLN A 955 " --> pdb=" O LYS A 951 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL A 956 " --> pdb=" O SER A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 997 Processing helix chain 'A' and resid 1013 through 1018 removed outlier: 3.942A pdb=" N THR A1016 " --> pdb=" O ASN A1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 630 Processing helix chain 'B' and resid 654 through 666 removed outlier: 3.700A pdb=" N VAL B 658 " --> pdb=" O ARG B 654 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE B 664 " --> pdb=" O PHE B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 702 removed outlier: 4.341A pdb=" N LEU B 688 " --> pdb=" O ARG B 684 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLN B 689 " --> pdb=" O MET B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 727 Processing helix chain 'B' and resid 749 through 766 removed outlier: 3.656A pdb=" N VAL B 753 " --> pdb=" O HIS B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 823 Processing helix chain 'B' and resid 840 through 851 Proline residue: B 846 - end of helix Processing helix chain 'B' and resid 867 through 869 No H-bonds generated for 'chain 'B' and resid 867 through 869' Processing helix chain 'B' and resid 870 through 886 Processing helix chain 'B' and resid 903 through 914 Processing helix chain 'B' and resid 915 through 918 Processing helix chain 'B' and resid 925 through 928 Processing helix chain 'B' and resid 929 through 934 removed outlier: 3.785A pdb=" N ARG B 933 " --> pdb=" O VAL B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 964 removed outlier: 5.165A pdb=" N VAL B 950 " --> pdb=" O THR B 946 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LYS B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 997 removed outlier: 3.515A pdb=" N SER B 997 " --> pdb=" O LEU B 993 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 707 through 712 removed outlier: 6.599A pdb=" N CYS A 644 " --> pdb=" O ILE A 672 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N GLY A 674 " --> pdb=" O CYS A 644 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL A 646 " --> pdb=" O GLY A 674 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N VAL A 676 " --> pdb=" O VAL A 646 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N GLY A 740 " --> pdb=" O LEU A 647 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE A 972 " --> pdb=" O ILE A1005 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ILE A1007 " --> pdb=" O ILE A 972 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE A 974 " --> pdb=" O ILE A1007 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASP A 831 " --> pdb=" O VAL A 973 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N THR A 975 " --> pdb=" O ASP A 831 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N TYR A 833 " --> pdb=" O THR A 975 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ILE A 830 " --> pdb=" O ARG A 861 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N PHE A 863 " --> pdb=" O ILE A 830 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE A 832 " --> pdb=" O PHE A 863 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE A 860 " --> pdb=" O GLU A 891 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N HIS A 893 " --> pdb=" O ILE A 860 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL A 862 " --> pdb=" O HIS A 893 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 707 through 713 removed outlier: 6.638A pdb=" N CYS B 644 " --> pdb=" O ILE B 672 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N GLY B 674 " --> pdb=" O CYS B 644 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL B 646 " --> pdb=" O GLY B 674 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N VAL B 676 " --> pdb=" O VAL B 646 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLY B 740 " --> pdb=" O LEU B 647 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE B 972 " --> pdb=" O ILE B1005 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ILE B1007 " --> pdb=" O ILE B 972 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE B 974 " --> pdb=" O ILE B1007 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 971 " --> pdb=" O THR B 829 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE B 830 " --> pdb=" O ARG B 861 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N PHE B 863 " --> pdb=" O ILE B 830 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE B 832 " --> pdb=" O PHE B 863 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N GLY B 865 " --> pdb=" O ILE B 832 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE B 860 " --> pdb=" O GLU B 891 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N HIS B 893 " --> pdb=" O ILE B 860 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL B 862 " --> pdb=" O HIS B 893 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LEU B 895 " --> pdb=" O VAL B 862 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL B 864 " --> pdb=" O LEU B 895 " (cutoff:3.500A) 538 hydrogen bonds defined for protein. 1554 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.53 Time building geometry restraints manager: 3.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3178 1.34 - 1.46: 2319 1.46 - 1.58: 4576 1.58 - 1.69: 28 1.69 - 1.81: 85 Bond restraints: 10186 Sorted by residual: bond pdb=" O1A ATP A1301 " pdb=" PA ATP A1301 " ideal model delta sigma weight residual 1.477 1.608 -0.131 1.10e-02 8.26e+03 1.42e+02 bond pdb=" O1A ATP B1101 " pdb=" PA ATP B1101 " ideal model delta sigma weight residual 1.477 1.605 -0.128 1.10e-02 8.26e+03 1.36e+02 bond pdb=" C6 ATP A1301 " pdb=" N6 ATP A1301 " ideal model delta sigma weight residual 1.337 1.440 -0.103 1.10e-02 8.26e+03 8.77e+01 bond pdb=" C6 ATP B1101 " pdb=" N6 ATP B1101 " ideal model delta sigma weight residual 1.337 1.440 -0.103 1.10e-02 8.26e+03 8.76e+01 bond pdb=" O1B ATP A1301 " pdb=" PB ATP A1301 " ideal model delta sigma weight residual 1.477 1.608 -0.131 2.20e-02 2.07e+03 3.57e+01 ... (remaining 10181 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.34: 13827 4.34 - 8.67: 31 8.67 - 13.01: 5 13.01 - 17.34: 2 17.34 - 21.68: 2 Bond angle restraints: 13867 Sorted by residual: angle pdb=" PB ATP A1301 " pdb=" O3B ATP A1301 " pdb=" PG ATP A1301 " ideal model delta sigma weight residual 139.87 118.19 21.68 1.00e+00 1.00e+00 4.70e+02 angle pdb=" PB ATP B1101 " pdb=" O3B ATP B1101 " pdb=" PG ATP B1101 " ideal model delta sigma weight residual 139.87 120.86 19.01 1.00e+00 1.00e+00 3.62e+02 angle pdb=" PA ATP A1301 " pdb=" O3A ATP A1301 " pdb=" PB ATP A1301 " ideal model delta sigma weight residual 136.83 119.75 17.08 1.00e+00 1.00e+00 2.92e+02 angle pdb=" PA ATP B1101 " pdb=" O3A ATP B1101 " pdb=" PB ATP B1101 " ideal model delta sigma weight residual 136.83 120.29 16.54 1.00e+00 1.00e+00 2.74e+02 angle pdb=" N1 ATP B1101 " pdb=" C2 ATP B1101 " pdb=" N3 ATP B1101 " ideal model delta sigma weight residual 128.69 120.70 7.99 1.00e+00 1.00e+00 6.39e+01 ... (remaining 13862 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 5131 17.76 - 35.52: 661 35.52 - 53.28: 181 53.28 - 71.05: 41 71.05 - 88.81: 15 Dihedral angle restraints: 6029 sinusoidal: 2369 harmonic: 3660 Sorted by residual: dihedral pdb=" CB CYS A 415 " pdb=" SG CYS A 415 " pdb=" SG CYS A 420 " pdb=" CB CYS A 420 " ideal model delta sinusoidal sigma weight residual -86.00 2.81 -88.81 1 1.00e+01 1.00e-02 9.40e+01 dihedral pdb=" CA PRO B1002 " pdb=" C PRO B1002 " pdb=" N PRO B1003 " pdb=" CA PRO B1003 " ideal model delta harmonic sigma weight residual 180.00 141.61 38.39 0 5.00e+00 4.00e-02 5.90e+01 dihedral pdb=" CB CYS A 429 " pdb=" SG CYS A 429 " pdb=" SG CYS A 435 " pdb=" CB CYS A 435 " ideal model delta sinusoidal sigma weight residual 93.00 38.27 54.73 1 1.00e+01 1.00e-02 4.06e+01 ... (remaining 6026 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 951 0.029 - 0.058: 392 0.058 - 0.087: 141 0.087 - 0.116: 71 0.116 - 0.145: 10 Chirality restraints: 1565 Sorted by residual: chirality pdb=" C2' ATP A1301 " pdb=" C1' ATP A1301 " pdb=" C3' ATP A1301 " pdb=" O2' ATP A1301 " both_signs ideal model delta sigma weight residual False -2.68 -2.54 -0.14 2.00e-01 2.50e+01 5.25e-01 chirality pdb=" C2' ATP B1101 " pdb=" C1' ATP B1101 " pdb=" C3' ATP B1101 " pdb=" O2' ATP B1101 " both_signs ideal model delta sigma weight residual False -2.68 -2.54 -0.14 2.00e-01 2.50e+01 5.06e-01 chirality pdb=" CB THR A 179 " pdb=" CA THR A 179 " pdb=" OG1 THR A 179 " pdb=" CG2 THR A 179 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.12 2.00e-01 2.50e+01 3.89e-01 ... (remaining 1562 not shown) Planarity restraints: 1741 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 984 " 0.031 5.00e-02 4.00e+02 4.82e-02 3.71e+00 pdb=" N PRO A 985 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 985 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 985 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B1002 " 0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO B1003 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B1003 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B1003 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 915 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO A 916 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 916 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 916 " -0.020 5.00e-02 4.00e+02 ... (remaining 1738 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 63 2.46 - 3.07: 7257 3.07 - 3.68: 15242 3.68 - 4.29: 23198 4.29 - 4.90: 38504 Nonbonded interactions: 84264 Sorted by model distance: nonbonded pdb=" O THR A 351 " pdb=" OH TYR A 539 " model vdw 1.847 3.040 nonbonded pdb=" O ASP A 88 " pdb=" NH2 ARG B 980 " model vdw 2.014 3.120 nonbonded pdb=" O PRO A 977 " pdb=" OH TYR A 989 " model vdw 2.038 3.040 nonbonded pdb=" OH TYR A 67 " pdb=" O HOH A1401 " model vdw 2.052 3.040 nonbonded pdb=" O GLY A 166 " pdb=" OG1 THR A 170 " model vdw 2.054 3.040 ... (remaining 84259 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.420 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.060 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: 0.020 Load rotamer database and sin/cos tables:15.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 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 : 0.006 0.131 10186 Z= 0.394 Angle : 0.711 21.679 13867 Z= 0.484 Chirality : 0.040 0.145 1565 Planarity : 0.004 0.048 1741 Dihedral : 17.533 84.610 3673 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 23.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.23 % Favored : 95.61 % Rotamer: Outliers : 2.72 % Allowed : 28.89 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.75 % 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: 1.32 (0.25), residues: 1252 helix: 2.20 (0.21), residues: 658 sheet: 0.54 (0.51), residues: 113 loop : -0.96 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 586 HIS 0.003 0.001 HIS A 636 PHE 0.014 0.001 PHE A 597 TYR 0.012 0.001 TYR A 965 ARG 0.008 0.000 ARG A 934 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 195 time to evaluate : 1.224 Fit side-chains revert: symmetry clash REVERT: A 154 LEU cc_start: 0.8275 (tp) cc_final: 0.7888 (tt) REVERT: A 164 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7373 (mm-40) REVERT: A 196 LYS cc_start: 0.7380 (ttmm) cc_final: 0.7066 (ttmt) REVERT: A 213 GLU cc_start: 0.6730 (mp0) cc_final: 0.6431 (mp0) REVERT: A 243 ASP cc_start: 0.7247 (m-30) cc_final: 0.6856 (m-30) REVERT: A 247 GLU cc_start: 0.6915 (tm-30) cc_final: 0.6676 (tt0) REVERT: A 310 ASP cc_start: 0.7508 (t0) cc_final: 0.7291 (t70) REVERT: A 331 ASP cc_start: 0.7297 (t0) cc_final: 0.6914 (t0) REVERT: A 345 ILE cc_start: 0.7261 (mt) cc_final: 0.6999 (mm) REVERT: A 416 GLU cc_start: 0.5942 (tm-30) cc_final: 0.5224 (tt0) REVERT: A 484 GLU cc_start: 0.6264 (mm-30) cc_final: 0.5884 (mt-10) REVERT: A 603 ILE cc_start: 0.7273 (tt) cc_final: 0.6933 (mt) REVERT: A 605 LYS cc_start: 0.7493 (tppp) cc_final: 0.7133 (tptt) REVERT: A 606 LYS cc_start: 0.6718 (mtmt) cc_final: 0.6198 (mmmt) REVERT: A 718 ARG cc_start: 0.7009 (mpp80) cc_final: 0.6169 (mmp80) REVERT: A 752 THR cc_start: 0.7945 (m) cc_final: 0.7655 (p) REVERT: A 767 ASN cc_start: 0.7918 (t0) cc_final: 0.7497 (t0) REVERT: A 777 GLU cc_start: 0.7134 (mp0) cc_final: 0.6677 (pm20) REVERT: A 827 LYS cc_start: 0.8130 (mmtm) cc_final: 0.7906 (mmtm) REVERT: A 857 LYS cc_start: 0.7846 (mmmm) cc_final: 0.6920 (mmtt) REVERT: A 947 LYS cc_start: 0.7146 (mttp) cc_final: 0.6800 (mttp) REVERT: A 949 ARG cc_start: 0.7013 (tpp80) cc_final: 0.6530 (tpp-160) REVERT: A 981 LYS cc_start: 0.6703 (OUTLIER) cc_final: 0.6204 (tptt) REVERT: A 999 ASP cc_start: 0.8194 (m-30) cc_final: 0.7970 (m-30) REVERT: A 1001 ARG cc_start: 0.7841 (ttm-80) cc_final: 0.7458 (ttm-80) REVERT: A 1011 GLN cc_start: 0.7953 (tp-100) cc_final: 0.7555 (mm-40) REVERT: A 1013 ASN cc_start: 0.8298 (t0) cc_final: 0.7864 (t0) REVERT: B 714 GLU cc_start: 0.7322 (mp0) cc_final: 0.6895 (mm-30) REVERT: B 820 ILE cc_start: 0.8191 (mp) cc_final: 0.7873 (pt) REVERT: B 827 LYS cc_start: 0.7927 (tppp) cc_final: 0.7270 (mmmt) REVERT: B 853 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.5981 (mtm-85) REVERT: B 857 LYS cc_start: 0.7801 (mmtt) cc_final: 0.7430 (tppt) REVERT: B 875 ARG cc_start: 0.6506 (ttp80) cc_final: 0.6115 (ttp-110) REVERT: B 903 ARG cc_start: 0.7516 (mmm-85) cc_final: 0.7262 (mtp-110) REVERT: B 905 GLU cc_start: 0.6778 (mp0) cc_final: 0.6405 (mp0) REVERT: B 911 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6891 (mt-10) REVERT: B 947 LYS cc_start: 0.7643 (mtpt) cc_final: 0.7236 (mmtt) REVERT: B 967 ARG cc_start: 0.7590 (tpp80) cc_final: 0.7248 (tpt170) REVERT: B 1001 ARG cc_start: 0.5569 (pmt-80) cc_final: 0.3151 (mmt90) outliers start: 28 outliers final: 15 residues processed: 215 average time/residue: 1.3127 time to fit residues: 301.8837 Evaluate side-chains 174 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 164 GLN Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 981 LYS Chi-restraints excluded: chain B residue 853 ARG Chi-restraints excluded: chain B residue 864 VAL Chi-restraints excluded: chain B residue 923 PHE Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain B residue 950 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN A 431 GLN A 900 GLN B 616 GLN B 873 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10186 Z= 0.261 Angle : 0.609 6.229 13867 Z= 0.319 Chirality : 0.044 0.183 1565 Planarity : 0.005 0.087 1741 Dihedral : 8.700 84.935 1486 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.07 % Favored : 95.77 % Rotamer: Outliers : 4.57 % Allowed : 24.51 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % 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: 1.24 (0.24), residues: 1252 helix: 1.98 (0.20), residues: 670 sheet: 0.42 (0.49), residues: 117 loop : -0.79 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 137 HIS 0.005 0.001 HIS B 761 PHE 0.014 0.002 PHE A 340 TYR 0.013 0.002 TYR B 626 ARG 0.007 0.001 ARG B1001 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 166 time to evaluate : 1.141 Fit side-chains revert: symmetry clash REVERT: A 196 LYS cc_start: 0.7380 (ttmm) cc_final: 0.7167 (ttmt) REVERT: A 213 GLU cc_start: 0.6758 (mp0) cc_final: 0.6506 (mp0) REVERT: A 243 ASP cc_start: 0.7151 (m-30) cc_final: 0.6811 (m-30) REVERT: A 258 ASP cc_start: 0.7296 (OUTLIER) cc_final: 0.6462 (m-30) REVERT: A 310 ASP cc_start: 0.7469 (t0) cc_final: 0.7218 (t70) REVERT: A 331 ASP cc_start: 0.7422 (t0) cc_final: 0.7083 (t0) REVERT: A 336 ASP cc_start: 0.7218 (OUTLIER) cc_final: 0.6365 (t0) REVERT: A 345 ILE cc_start: 0.7506 (mt) cc_final: 0.7214 (mm) REVERT: A 416 GLU cc_start: 0.6003 (tm-30) cc_final: 0.5261 (tt0) REVERT: A 484 GLU cc_start: 0.6644 (mm-30) cc_final: 0.6405 (mt-10) REVERT: A 485 ASP cc_start: 0.6956 (m-30) cc_final: 0.6675 (m-30) REVERT: A 530 ILE cc_start: 0.6467 (OUTLIER) cc_final: 0.6264 (mm) REVERT: A 605 LYS cc_start: 0.7459 (tppp) cc_final: 0.7124 (tptt) REVERT: A 606 LYS cc_start: 0.6837 (mtmt) cc_final: 0.6558 (tttt) REVERT: A 718 ARG cc_start: 0.7011 (mpp80) cc_final: 0.6228 (mmp80) REVERT: A 731 ARG cc_start: 0.7382 (ttm-80) cc_final: 0.6621 (mtt90) REVERT: A 752 THR cc_start: 0.8034 (OUTLIER) cc_final: 0.7794 (p) REVERT: A 767 ASN cc_start: 0.7951 (t0) cc_final: 0.7745 (t0) REVERT: A 777 GLU cc_start: 0.7179 (mp0) cc_final: 0.6706 (pm20) REVERT: A 824 GLU cc_start: 0.6590 (mp0) cc_final: 0.6004 (mm-30) REVERT: A 827 LYS cc_start: 0.8132 (mmtm) cc_final: 0.7816 (mmtm) REVERT: A 857 LYS cc_start: 0.7885 (mmmm) cc_final: 0.6911 (mmtt) REVERT: A 947 LYS cc_start: 0.7584 (mttp) cc_final: 0.7291 (mttp) REVERT: A 949 ARG cc_start: 0.6890 (tpp80) cc_final: 0.6443 (tpp-160) REVERT: A 999 ASP cc_start: 0.8245 (m-30) cc_final: 0.7950 (m-30) REVERT: A 1001 ARG cc_start: 0.7853 (ttm-80) cc_final: 0.7620 (ttm-80) REVERT: A 1011 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7763 (mm-40) REVERT: A 1012 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7812 (tt0) REVERT: A 1013 ASN cc_start: 0.8292 (t0) cc_final: 0.7885 (t0) REVERT: B 667 ASN cc_start: 0.7562 (p0) cc_final: 0.7360 (p0) REVERT: B 714 GLU cc_start: 0.7225 (mp0) cc_final: 0.6817 (mm-30) REVERT: B 853 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.6952 (pmt170) REVERT: B 857 LYS cc_start: 0.7831 (mmtt) cc_final: 0.7557 (tppt) REVERT: B 875 ARG cc_start: 0.6389 (ttp80) cc_final: 0.5258 (ttm110) REVERT: B 905 GLU cc_start: 0.6900 (mp0) cc_final: 0.6537 (mp0) REVERT: B 911 GLU cc_start: 0.7096 (mt-10) cc_final: 0.6895 (mt-10) REVERT: B 947 LYS cc_start: 0.7829 (mtpt) cc_final: 0.7338 (mmtt) REVERT: B 967 ARG cc_start: 0.7620 (tpp80) cc_final: 0.7314 (tpt170) REVERT: B 1001 ARG cc_start: 0.5198 (OUTLIER) cc_final: 0.3198 (mmt90) outliers start: 47 outliers final: 15 residues processed: 197 average time/residue: 1.3052 time to fit residues: 275.5460 Evaluate side-chains 172 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain A residue 987 SER Chi-restraints excluded: chain A residue 1011 GLN Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 853 ARG Chi-restraints excluded: chain B residue 872 ASP Chi-restraints excluded: chain B residue 923 PHE Chi-restraints excluded: chain B residue 1001 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 chunk 102 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 GLN B 959 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10186 Z= 0.354 Angle : 0.637 6.320 13867 Z= 0.331 Chirality : 0.046 0.199 1565 Planarity : 0.005 0.071 1741 Dihedral : 8.794 80.044 1471 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.99 % Favored : 95.85 % Rotamer: Outliers : 5.64 % Allowed : 22.47 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % 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: 0.96 (0.24), residues: 1252 helix: 1.74 (0.20), residues: 668 sheet: 0.39 (0.47), residues: 116 loop : -0.92 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 137 HIS 0.005 0.001 HIS B 761 PHE 0.017 0.002 PHE A 340 TYR 0.016 0.002 TYR B 626 ARG 0.007 0.001 ARG B1001 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 146 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7160 (mp0) cc_final: 0.6886 (mp0) REVERT: A 243 ASP cc_start: 0.7072 (m-30) cc_final: 0.6746 (m-30) REVERT: A 309 GLU cc_start: 0.7480 (tp30) cc_final: 0.7093 (mp0) REVERT: A 310 ASP cc_start: 0.7428 (t0) cc_final: 0.7156 (t70) REVERT: A 331 ASP cc_start: 0.7523 (t0) cc_final: 0.7172 (t0) REVERT: A 336 ASP cc_start: 0.7049 (OUTLIER) cc_final: 0.6204 (t0) REVERT: A 345 ILE cc_start: 0.7561 (OUTLIER) cc_final: 0.7251 (mm) REVERT: A 416 GLU cc_start: 0.6519 (tm-30) cc_final: 0.5276 (tt0) REVERT: A 484 GLU cc_start: 0.6697 (mm-30) cc_final: 0.6478 (mt-10) REVERT: A 605 LYS cc_start: 0.7492 (tppp) cc_final: 0.7144 (tptt) REVERT: A 606 LYS cc_start: 0.6836 (mtmt) cc_final: 0.6553 (mttt) REVERT: A 665 THR cc_start: 0.7970 (OUTLIER) cc_final: 0.7650 (m) REVERT: A 718 ARG cc_start: 0.7080 (mpp80) cc_final: 0.6239 (mmp80) REVERT: A 731 ARG cc_start: 0.7575 (ttm-80) cc_final: 0.6679 (mtt90) REVERT: A 752 THR cc_start: 0.8042 (OUTLIER) cc_final: 0.7836 (p) REVERT: A 777 GLU cc_start: 0.7144 (mp0) cc_final: 0.6620 (pm20) REVERT: A 824 GLU cc_start: 0.6420 (mp0) cc_final: 0.5916 (mm-30) REVERT: A 827 LYS cc_start: 0.8123 (mmtm) cc_final: 0.7812 (mmtm) REVERT: A 857 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.6949 (mmtt) REVERT: A 947 LYS cc_start: 0.7668 (mttp) cc_final: 0.7414 (mttp) REVERT: A 949 ARG cc_start: 0.6925 (tpp80) cc_final: 0.6414 (tpp-160) REVERT: A 967 ARG cc_start: 0.7949 (mtm-85) cc_final: 0.7619 (mtm-85) REVERT: A 999 ASP cc_start: 0.8160 (m-30) cc_final: 0.7851 (m-30) REVERT: A 1001 ARG cc_start: 0.7897 (ttm-80) cc_final: 0.7648 (ttm-80) REVERT: A 1011 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7655 (mm-40) REVERT: A 1012 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7698 (tt0) REVERT: B 714 GLU cc_start: 0.7165 (mp0) cc_final: 0.6754 (mm-30) REVERT: B 827 LYS cc_start: 0.8024 (tppp) cc_final: 0.7247 (mmmt) REVERT: B 853 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.6916 (pmt170) REVERT: B 857 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7521 (mmtm) REVERT: B 875 ARG cc_start: 0.6332 (ttp80) cc_final: 0.5261 (ttm110) REVERT: B 903 ARG cc_start: 0.7063 (mmm-85) cc_final: 0.6740 (mtp-110) REVERT: B 905 GLU cc_start: 0.6900 (mp0) cc_final: 0.6432 (mp0) REVERT: B 911 GLU cc_start: 0.7218 (mt-10) cc_final: 0.7002 (mt-10) REVERT: B 947 LYS cc_start: 0.7902 (mtpt) cc_final: 0.7412 (mttt) REVERT: B 1001 ARG cc_start: 0.5371 (OUTLIER) cc_final: 0.3069 (mpt-90) outliers start: 58 outliers final: 20 residues processed: 181 average time/residue: 1.3880 time to fit residues: 268.9009 Evaluate side-chains 169 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain A residue 857 LYS Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 898 ILE Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain A residue 1011 GLN Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 853 ARG Chi-restraints excluded: chain B residue 857 LYS Chi-restraints excluded: chain B residue 923 PHE Chi-restraints excluded: chain B residue 1001 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 59 optimal weight: 9.9990 chunk 12 optimal weight: 0.6980 chunk 54 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 32 optimal weight: 0.0030 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10186 Z= 0.196 Angle : 0.545 6.196 13867 Z= 0.285 Chirality : 0.042 0.160 1565 Planarity : 0.005 0.062 1741 Dihedral : 8.458 74.433 1469 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.91 % Favored : 96.01 % Rotamer: Outliers : 4.28 % Allowed : 23.05 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % 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: 1.07 (0.24), residues: 1252 helix: 1.82 (0.20), residues: 678 sheet: 0.38 (0.47), residues: 116 loop : -0.90 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 137 HIS 0.003 0.001 HIS B 761 PHE 0.011 0.001 PHE B 664 TYR 0.012 0.001 TYR A 626 ARG 0.006 0.001 ARG B 949 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 148 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7193 (mp0) cc_final: 0.6876 (mp0) REVERT: A 142 MET cc_start: 0.7783 (ttp) cc_final: 0.7487 (ttt) REVERT: A 232 MET cc_start: 0.6849 (mtp) cc_final: 0.6642 (mtp) REVERT: A 243 ASP cc_start: 0.6970 (m-30) cc_final: 0.6647 (m-30) REVERT: A 309 GLU cc_start: 0.7477 (tp30) cc_final: 0.7116 (mp0) REVERT: A 310 ASP cc_start: 0.7407 (t0) cc_final: 0.7161 (t70) REVERT: A 331 ASP cc_start: 0.7429 (t0) cc_final: 0.7082 (t0) REVERT: A 336 ASP cc_start: 0.7027 (OUTLIER) cc_final: 0.6310 (t0) REVERT: A 345 ILE cc_start: 0.7513 (OUTLIER) cc_final: 0.7258 (mm) REVERT: A 416 GLU cc_start: 0.6266 (tm-30) cc_final: 0.5636 (tt0) REVERT: A 605 LYS cc_start: 0.7457 (tppp) cc_final: 0.7187 (tptt) REVERT: A 606 LYS cc_start: 0.6832 (mtmt) cc_final: 0.6548 (ttmt) REVERT: A 665 THR cc_start: 0.7879 (OUTLIER) cc_final: 0.7517 (m) REVERT: A 718 ARG cc_start: 0.6994 (mpp80) cc_final: 0.6167 (mmp80) REVERT: A 731 ARG cc_start: 0.7428 (ttm-80) cc_final: 0.6491 (mtt90) REVERT: A 777 GLU cc_start: 0.7185 (mp0) cc_final: 0.6582 (pm20) REVERT: A 824 GLU cc_start: 0.6342 (mp0) cc_final: 0.5870 (mm-30) REVERT: A 827 LYS cc_start: 0.8128 (mmtm) cc_final: 0.7823 (mmtm) REVERT: A 853 ARG cc_start: 0.7456 (pmm150) cc_final: 0.6684 (mtm-85) REVERT: A 857 LYS cc_start: 0.7895 (mmmm) cc_final: 0.6931 (mmtt) REVERT: A 947 LYS cc_start: 0.7790 (mttp) cc_final: 0.7554 (mttp) REVERT: A 949 ARG cc_start: 0.6923 (tpp80) cc_final: 0.6502 (tpp-160) REVERT: A 967 ARG cc_start: 0.7938 (mtm-85) cc_final: 0.7525 (mtm-85) REVERT: A 999 ASP cc_start: 0.8171 (m-30) cc_final: 0.7896 (m-30) REVERT: A 1001 ARG cc_start: 0.7873 (ttm-80) cc_final: 0.7640 (ttm-80) REVERT: A 1011 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7711 (mm-40) REVERT: B 667 ASN cc_start: 0.7462 (p0) cc_final: 0.6292 (m110) REVERT: B 714 GLU cc_start: 0.7174 (mp0) cc_final: 0.6909 (mp0) REVERT: B 827 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7221 (mmmt) REVERT: B 853 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.6947 (pmt170) REVERT: B 857 LYS cc_start: 0.7834 (mmtt) cc_final: 0.7447 (tppt) REVERT: B 875 ARG cc_start: 0.6348 (ttp80) cc_final: 0.5325 (ttm110) REVERT: B 905 GLU cc_start: 0.6899 (mp0) cc_final: 0.6170 (pm20) REVERT: B 911 GLU cc_start: 0.7248 (mt-10) cc_final: 0.7047 (mt-10) REVERT: B 947 LYS cc_start: 0.7855 (mtpt) cc_final: 0.7259 (mmtp) REVERT: B 1001 ARG cc_start: 0.5218 (OUTLIER) cc_final: 0.3100 (mpt-90) outliers start: 44 outliers final: 15 residues processed: 174 average time/residue: 1.3056 time to fit residues: 243.5491 Evaluate side-chains 162 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 1011 GLN Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1016 THR Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 827 LYS Chi-restraints excluded: chain B residue 853 ARG Chi-restraints excluded: chain B residue 923 PHE Chi-restraints excluded: chain B residue 1001 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 0.8980 chunk 69 optimal weight: 0.1980 chunk 1 optimal weight: 0.0670 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 overall best weight: 1.0320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 GLN B 616 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10186 Z= 0.210 Angle : 0.549 6.103 13867 Z= 0.286 Chirality : 0.042 0.201 1565 Planarity : 0.004 0.055 1741 Dihedral : 8.412 70.801 1469 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.91 % Favored : 96.01 % Rotamer: Outliers : 3.99 % Allowed : 23.35 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % 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: 1.10 (0.24), residues: 1252 helix: 1.88 (0.20), residues: 672 sheet: 0.36 (0.47), residues: 116 loop : -0.91 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 137 HIS 0.003 0.001 HIS B 761 PHE 0.012 0.001 PHE B 664 TYR 0.012 0.001 TYR A 626 ARG 0.005 0.000 ARG A 851 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 144 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7189 (mp0) cc_final: 0.6925 (mp0) REVERT: A 232 MET cc_start: 0.6862 (OUTLIER) cc_final: 0.6657 (mtp) REVERT: A 243 ASP cc_start: 0.6968 (m-30) cc_final: 0.6648 (m-30) REVERT: A 310 ASP cc_start: 0.7399 (t0) cc_final: 0.7123 (t70) REVERT: A 331 ASP cc_start: 0.7507 (t0) cc_final: 0.7163 (t0) REVERT: A 336 ASP cc_start: 0.7084 (OUTLIER) cc_final: 0.6325 (t0) REVERT: A 345 ILE cc_start: 0.7517 (OUTLIER) cc_final: 0.7262 (mm) REVERT: A 416 GLU cc_start: 0.6286 (tm-30) cc_final: 0.5590 (tt0) REVERT: A 431 GLN cc_start: 0.7192 (mm-40) cc_final: 0.6958 (mp10) REVERT: A 562 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.7461 (mt0) REVERT: A 605 LYS cc_start: 0.7415 (tppp) cc_final: 0.7150 (tptt) REVERT: A 606 LYS cc_start: 0.6773 (mtmt) cc_final: 0.6514 (ttmt) REVERT: A 665 THR cc_start: 0.7930 (OUTLIER) cc_final: 0.7569 (m) REVERT: A 718 ARG cc_start: 0.7010 (tpp80) cc_final: 0.6171 (mmp80) REVERT: A 731 ARG cc_start: 0.7415 (ttm-80) cc_final: 0.6646 (mtt90) REVERT: A 776 ARG cc_start: 0.7045 (ptm160) cc_final: 0.6840 (ptp-110) REVERT: A 777 GLU cc_start: 0.7193 (mp0) cc_final: 0.6594 (pm20) REVERT: A 779 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6872 (mm) REVERT: A 824 GLU cc_start: 0.6315 (mp0) cc_final: 0.5859 (mm-30) REVERT: A 827 LYS cc_start: 0.8139 (mmtm) cc_final: 0.7861 (mmtm) REVERT: A 853 ARG cc_start: 0.7467 (pmm150) cc_final: 0.6739 (mtm-85) REVERT: A 857 LYS cc_start: 0.7895 (mmmm) cc_final: 0.6928 (mmtt) REVERT: A 947 LYS cc_start: 0.7782 (mttp) cc_final: 0.7576 (mttp) REVERT: A 949 ARG cc_start: 0.6908 (tpp80) cc_final: 0.6502 (tpp-160) REVERT: A 967 ARG cc_start: 0.7936 (mtm-85) cc_final: 0.7522 (mtm-85) REVERT: A 999 ASP cc_start: 0.8158 (m-30) cc_final: 0.7877 (m-30) REVERT: A 1011 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7708 (mm-40) REVERT: B 667 ASN cc_start: 0.7412 (p0) cc_final: 0.6563 (m-40) REVERT: B 827 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7231 (mmmt) REVERT: B 853 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.6909 (pmt170) REVERT: B 857 LYS cc_start: 0.7818 (mmtt) cc_final: 0.7542 (mmtm) REVERT: B 875 ARG cc_start: 0.6351 (ttp80) cc_final: 0.5318 (ttm110) REVERT: B 905 GLU cc_start: 0.6932 (mp0) cc_final: 0.6183 (pm20) REVERT: B 911 GLU cc_start: 0.7239 (mt-10) cc_final: 0.7037 (mt-10) REVERT: B 947 LYS cc_start: 0.7832 (mtpt) cc_final: 0.7330 (mmtt) REVERT: B 1001 ARG cc_start: 0.5163 (OUTLIER) cc_final: 0.3134 (mpt-90) outliers start: 41 outliers final: 16 residues processed: 169 average time/residue: 1.3356 time to fit residues: 241.6314 Evaluate side-chains 165 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 562 GLN Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 965 TYR Chi-restraints excluded: chain A residue 1011 GLN Chi-restraints excluded: chain A residue 1016 THR Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 827 LYS Chi-restraints excluded: chain B residue 853 ARG Chi-restraints excluded: chain B residue 923 PHE Chi-restraints excluded: chain B residue 1001 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.1980 chunk 109 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 101 optimal weight: 0.4980 chunk 56 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 744 ASN B 616 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10186 Z= 0.236 Angle : 0.559 6.100 13867 Z= 0.292 Chirality : 0.042 0.182 1565 Planarity : 0.005 0.051 1741 Dihedral : 8.456 68.274 1469 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.91 % Favored : 96.01 % Rotamer: Outliers : 4.18 % Allowed : 23.15 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % 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: 1.07 (0.24), residues: 1252 helix: 1.85 (0.20), residues: 672 sheet: 0.27 (0.47), residues: 118 loop : -0.90 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 137 HIS 0.003 0.001 HIS B 761 PHE 0.015 0.001 PHE A 597 TYR 0.012 0.002 TYR B 626 ARG 0.009 0.001 ARG A1001 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 143 time to evaluate : 1.162 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7201 (mp0) cc_final: 0.6910 (mp0) REVERT: A 142 MET cc_start: 0.7826 (ttp) cc_final: 0.7605 (ttt) REVERT: A 232 MET cc_start: 0.6856 (OUTLIER) cc_final: 0.6652 (mtp) REVERT: A 243 ASP cc_start: 0.6911 (m-30) cc_final: 0.6617 (m-30) REVERT: A 310 ASP cc_start: 0.7366 (t0) cc_final: 0.7092 (t70) REVERT: A 331 ASP cc_start: 0.7519 (t0) cc_final: 0.7180 (t0) REVERT: A 336 ASP cc_start: 0.7076 (OUTLIER) cc_final: 0.6358 (t0) REVERT: A 345 ILE cc_start: 0.7516 (mt) cc_final: 0.7257 (mm) REVERT: A 416 GLU cc_start: 0.6602 (tm-30) cc_final: 0.5674 (tt0) REVERT: A 431 GLN cc_start: 0.7225 (mm-40) cc_final: 0.6993 (mp10) REVERT: A 562 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.7123 (mt0) REVERT: A 605 LYS cc_start: 0.7422 (tppp) cc_final: 0.7160 (tptt) REVERT: A 606 LYS cc_start: 0.6782 (mtmt) cc_final: 0.6489 (mttt) REVERT: A 665 THR cc_start: 0.7881 (OUTLIER) cc_final: 0.7528 (m) REVERT: A 718 ARG cc_start: 0.6982 (tpp80) cc_final: 0.6120 (mmp80) REVERT: A 731 ARG cc_start: 0.7480 (ttm-80) cc_final: 0.6618 (mtt90) REVERT: A 776 ARG cc_start: 0.7066 (ptm160) cc_final: 0.6843 (ptp-110) REVERT: A 777 GLU cc_start: 0.7142 (mp0) cc_final: 0.6550 (pm20) REVERT: A 824 GLU cc_start: 0.6252 (mp0) cc_final: 0.5850 (mm-30) REVERT: A 827 LYS cc_start: 0.8117 (mmtm) cc_final: 0.7859 (mmtm) REVERT: A 853 ARG cc_start: 0.7406 (pmm150) cc_final: 0.6814 (mtm-85) REVERT: A 857 LYS cc_start: 0.7897 (mmmm) cc_final: 0.6937 (mmtt) REVERT: A 947 LYS cc_start: 0.7766 (mttp) cc_final: 0.7557 (mttp) REVERT: A 949 ARG cc_start: 0.6900 (tpp80) cc_final: 0.6527 (tpp-160) REVERT: A 967 ARG cc_start: 0.7920 (mtm-85) cc_final: 0.7636 (mtm-85) REVERT: A 999 ASP cc_start: 0.8163 (m-30) cc_final: 0.7893 (m-30) REVERT: A 1011 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7687 (mm-40) REVERT: B 667 ASN cc_start: 0.7422 (p0) cc_final: 0.6902 (m-40) REVERT: B 827 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7247 (mmmt) REVERT: B 853 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.6960 (pmt170) REVERT: B 857 LYS cc_start: 0.7828 (mmtt) cc_final: 0.7593 (mmtm) REVERT: B 875 ARG cc_start: 0.6325 (ttp80) cc_final: 0.5310 (ttm110) REVERT: B 905 GLU cc_start: 0.6952 (mp0) cc_final: 0.6187 (pm20) REVERT: B 911 GLU cc_start: 0.7289 (mt-10) cc_final: 0.7087 (mt-10) REVERT: B 947 LYS cc_start: 0.7845 (mtpt) cc_final: 0.7265 (mmtp) REVERT: B 1001 ARG cc_start: 0.5139 (OUTLIER) cc_final: 0.3030 (mpt-90) outliers start: 43 outliers final: 19 residues processed: 169 average time/residue: 1.3443 time to fit residues: 243.3744 Evaluate side-chains 163 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 232 MET Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 562 GLN Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 898 ILE Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 965 TYR Chi-restraints excluded: chain A residue 1011 GLN Chi-restraints excluded: chain A residue 1016 THR Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 827 LYS Chi-restraints excluded: chain B residue 853 ARG Chi-restraints excluded: chain B residue 923 PHE Chi-restraints excluded: chain B residue 1001 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 75 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 816 GLN B 616 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 10186 Z= 0.445 Angle : 0.674 7.067 13867 Z= 0.349 Chirality : 0.048 0.182 1565 Planarity : 0.006 0.059 1741 Dihedral : 8.915 69.242 1469 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.47 % Favored : 95.45 % Rotamer: Outliers : 4.47 % Allowed : 22.18 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % 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: 0.76 (0.23), residues: 1252 helix: 1.57 (0.20), residues: 668 sheet: 0.17 (0.46), residues: 121 loop : -0.99 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 137 HIS 0.004 0.001 HIS B 890 PHE 0.018 0.002 PHE A 597 TYR 0.016 0.002 TYR B 626 ARG 0.012 0.001 ARG A1001 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 138 time to evaluate : 1.215 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7253 (mp0) cc_final: 0.6973 (mp0) REVERT: A 243 ASP cc_start: 0.6972 (m-30) cc_final: 0.6657 (m-30) REVERT: A 310 ASP cc_start: 0.7423 (t0) cc_final: 0.7174 (t70) REVERT: A 331 ASP cc_start: 0.7621 (t0) cc_final: 0.7287 (t0) REVERT: A 336 ASP cc_start: 0.7089 (OUTLIER) cc_final: 0.6342 (t0) REVERT: A 345 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.7243 (mm) REVERT: A 406 ASP cc_start: 0.6502 (m-30) cc_final: 0.6261 (m-30) REVERT: A 416 GLU cc_start: 0.6698 (tm-30) cc_final: 0.5829 (tt0) REVERT: A 605 LYS cc_start: 0.7470 (tppp) cc_final: 0.7212 (tptt) REVERT: A 606 LYS cc_start: 0.6779 (mtmt) cc_final: 0.6487 (mttt) REVERT: A 718 ARG cc_start: 0.6935 (tpp80) cc_final: 0.6077 (mmp80) REVERT: A 776 ARG cc_start: 0.7014 (ptm160) cc_final: 0.6750 (ptp-110) REVERT: A 777 GLU cc_start: 0.7071 (mp0) cc_final: 0.6464 (pm20) REVERT: A 824 GLU cc_start: 0.6295 (mp0) cc_final: 0.5857 (mm-30) REVERT: A 827 LYS cc_start: 0.8125 (mmtm) cc_final: 0.7884 (mmtm) REVERT: A 853 ARG cc_start: 0.7378 (pmm150) cc_final: 0.6802 (mtm-85) REVERT: A 857 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.6942 (mmtt) REVERT: A 947 LYS cc_start: 0.7687 (mttp) cc_final: 0.7381 (mttp) REVERT: A 949 ARG cc_start: 0.6929 (tpp80) cc_final: 0.6491 (tpp-160) REVERT: A 999 ASP cc_start: 0.8162 (m-30) cc_final: 0.7893 (m-30) REVERT: A 1011 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7778 (tp40) REVERT: B 827 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7218 (mmmt) REVERT: B 853 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.6968 (pmt170) REVERT: B 857 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7633 (mmtm) REVERT: B 875 ARG cc_start: 0.6324 (ttp80) cc_final: 0.5319 (ttm110) REVERT: B 903 ARG cc_start: 0.7079 (mmm-85) cc_final: 0.6717 (mtp-110) REVERT: B 905 GLU cc_start: 0.6996 (mp0) cc_final: 0.6496 (mp0) REVERT: B 911 GLU cc_start: 0.7425 (mt-10) cc_final: 0.7208 (mt-10) REVERT: B 947 LYS cc_start: 0.7926 (mtpt) cc_final: 0.7334 (mmtt) REVERT: B 1001 ARG cc_start: 0.5373 (OUTLIER) cc_final: 0.2881 (mpt-90) outliers start: 46 outliers final: 23 residues processed: 166 average time/residue: 1.3333 time to fit residues: 237.3882 Evaluate side-chains 168 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 816 GLN Chi-restraints excluded: chain A residue 857 LYS Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 898 ILE Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 1011 GLN Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1016 THR Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 827 LYS Chi-restraints excluded: chain B residue 853 ARG Chi-restraints excluded: chain B residue 857 LYS Chi-restraints excluded: chain B residue 923 PHE Chi-restraints excluded: chain B residue 1001 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10186 Z= 0.201 Angle : 0.555 6.318 13867 Z= 0.291 Chirality : 0.042 0.175 1565 Planarity : 0.005 0.058 1741 Dihedral : 8.505 70.588 1469 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.51 % Favored : 96.41 % Rotamer: Outliers : 3.50 % Allowed : 22.37 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % 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 (0.24), residues: 1252 helix: 1.82 (0.20), residues: 671 sheet: 0.28 (0.47), residues: 118 loop : -0.92 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 137 HIS 0.002 0.001 HIS B 761 PHE 0.020 0.001 PHE A 597 TYR 0.012 0.001 TYR A 626 ARG 0.013 0.001 ARG A1001 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 139 time to evaluate : 1.202 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7272 (mp0) cc_final: 0.6971 (mp0) REVERT: A 243 ASP cc_start: 0.6899 (m-30) cc_final: 0.6576 (m-30) REVERT: A 310 ASP cc_start: 0.7386 (t0) cc_final: 0.7114 (t70) REVERT: A 331 ASP cc_start: 0.7436 (t0) cc_final: 0.7084 (t0) REVERT: A 336 ASP cc_start: 0.7130 (OUTLIER) cc_final: 0.6419 (t0) REVERT: A 345 ILE cc_start: 0.7549 (OUTLIER) cc_final: 0.7320 (mm) REVERT: A 406 ASP cc_start: 0.6471 (m-30) cc_final: 0.6245 (m-30) REVERT: A 416 GLU cc_start: 0.6622 (tm-30) cc_final: 0.5736 (tt0) REVERT: A 605 LYS cc_start: 0.7406 (tppp) cc_final: 0.7143 (tptt) REVERT: A 606 LYS cc_start: 0.6734 (mtmt) cc_final: 0.6448 (mttt) REVERT: A 718 ARG cc_start: 0.6929 (tpp80) cc_final: 0.6108 (mmp80) REVERT: A 776 ARG cc_start: 0.7039 (ptm160) cc_final: 0.6765 (ptp-110) REVERT: A 777 GLU cc_start: 0.7079 (mp0) cc_final: 0.6563 (pm20) REVERT: A 824 GLU cc_start: 0.6268 (mp0) cc_final: 0.5792 (mm-30) REVERT: A 827 LYS cc_start: 0.8172 (mmtm) cc_final: 0.7933 (mmtm) REVERT: A 853 ARG cc_start: 0.7376 (pmm150) cc_final: 0.6930 (mtm-85) REVERT: A 857 LYS cc_start: 0.7887 (mmmm) cc_final: 0.6922 (mmtt) REVERT: A 918 ARG cc_start: 0.7442 (mtp85) cc_final: 0.7239 (mtp85) REVERT: A 947 LYS cc_start: 0.7758 (mttp) cc_final: 0.7400 (mttp) REVERT: A 949 ARG cc_start: 0.6955 (tpp80) cc_final: 0.6533 (tpp-160) REVERT: A 967 ARG cc_start: 0.7859 (mtm-85) cc_final: 0.7545 (mmm-85) REVERT: A 999 ASP cc_start: 0.8165 (m-30) cc_final: 0.7878 (m-30) REVERT: A 1011 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7592 (tp40) REVERT: B 667 ASN cc_start: 0.7346 (p0) cc_final: 0.6857 (m-40) REVERT: B 827 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7221 (mmmt) REVERT: B 853 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.6906 (pmt170) REVERT: B 857 LYS cc_start: 0.7824 (mmtt) cc_final: 0.7516 (tppt) REVERT: B 875 ARG cc_start: 0.6341 (ttp80) cc_final: 0.5348 (ttm110) REVERT: B 905 GLU cc_start: 0.7003 (mp0) cc_final: 0.6249 (pm20) REVERT: B 911 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7194 (mt-10) REVERT: B 947 LYS cc_start: 0.7862 (mtpt) cc_final: 0.7278 (mmtt) REVERT: B 1001 ARG cc_start: 0.5246 (OUTLIER) cc_final: 0.3019 (mpt-90) outliers start: 36 outliers final: 19 residues processed: 160 average time/residue: 1.3263 time to fit residues: 227.6941 Evaluate side-chains 160 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 898 ILE Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 965 TYR Chi-restraints excluded: chain A residue 1011 GLN Chi-restraints excluded: chain A residue 1016 THR Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 827 LYS Chi-restraints excluded: chain B residue 853 ARG Chi-restraints excluded: chain B residue 923 PHE Chi-restraints excluded: chain B residue 1001 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 2.9990 chunk 116 optimal weight: 0.1980 chunk 68 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 chunk 102 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 74 optimal weight: 0.0470 chunk 119 optimal weight: 2.9990 overall best weight: 0.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10186 Z= 0.166 Angle : 0.525 6.181 13867 Z= 0.275 Chirality : 0.041 0.212 1565 Planarity : 0.004 0.054 1741 Dihedral : 8.072 68.668 1468 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.91 % Favored : 96.01 % Rotamer: Outliers : 2.33 % Allowed : 24.12 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % 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: 1.16 (0.24), residues: 1252 helix: 1.99 (0.20), residues: 671 sheet: 0.30 (0.47), residues: 121 loop : -0.96 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 137 HIS 0.002 0.001 HIS B 761 PHE 0.022 0.001 PHE A 597 TYR 0.011 0.001 TYR A 626 ARG 0.014 0.001 ARG A1001 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 1.178 Fit side-chains REVERT: A 68 GLU cc_start: 0.7228 (mp0) cc_final: 0.6951 (mp0) REVERT: A 243 ASP cc_start: 0.6874 (m-30) cc_final: 0.6560 (m-30) REVERT: A 258 ASP cc_start: 0.7221 (OUTLIER) cc_final: 0.6459 (m-30) REVERT: A 331 ASP cc_start: 0.7474 (t0) cc_final: 0.7122 (t0) REVERT: A 336 ASP cc_start: 0.7061 (OUTLIER) cc_final: 0.6445 (t0) REVERT: A 345 ILE cc_start: 0.7437 (mt) cc_final: 0.7227 (mm) REVERT: A 406 ASP cc_start: 0.6462 (m-30) cc_final: 0.6186 (m-30) REVERT: A 416 GLU cc_start: 0.6572 (tm-30) cc_final: 0.5488 (tt0) REVERT: A 605 LYS cc_start: 0.7445 (tppp) cc_final: 0.7167 (tptt) REVERT: A 606 LYS cc_start: 0.6661 (mtmt) cc_final: 0.6384 (mttt) REVERT: A 718 ARG cc_start: 0.6924 (tpp80) cc_final: 0.6112 (mmp80) REVERT: A 776 ARG cc_start: 0.7054 (ptm160) cc_final: 0.6753 (ptp-110) REVERT: A 777 GLU cc_start: 0.7090 (mp0) cc_final: 0.6588 (pm20) REVERT: A 824 GLU cc_start: 0.6257 (mp0) cc_final: 0.5791 (mm-30) REVERT: A 827 LYS cc_start: 0.8169 (mmtm) cc_final: 0.7945 (mmtm) REVERT: A 853 ARG cc_start: 0.7351 (pmm150) cc_final: 0.6902 (mtm-85) REVERT: A 857 LYS cc_start: 0.7875 (mmmm) cc_final: 0.6949 (mmtt) REVERT: A 947 LYS cc_start: 0.7842 (mttp) cc_final: 0.7517 (mttp) REVERT: A 949 ARG cc_start: 0.6915 (tpp80) cc_final: 0.6499 (tpp-160) REVERT: A 967 ARG cc_start: 0.7871 (mtm-85) cc_final: 0.7565 (mmm-85) REVERT: A 999 ASP cc_start: 0.8167 (m-30) cc_final: 0.7887 (m-30) REVERT: A 1001 ARG cc_start: 0.8013 (ttm110) cc_final: 0.7626 (ttm110) REVERT: A 1011 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7585 (tp40) REVERT: B 667 ASN cc_start: 0.7277 (p0) cc_final: 0.6941 (m-40) REVERT: B 827 LYS cc_start: 0.8025 (tppp) cc_final: 0.7201 (mmmt) REVERT: B 853 ARG cc_start: 0.7288 (OUTLIER) cc_final: 0.6883 (pmt170) REVERT: B 857 LYS cc_start: 0.7832 (mmtt) cc_final: 0.7509 (tppt) REVERT: B 875 ARG cc_start: 0.6306 (ttp80) cc_final: 0.5294 (ttm110) REVERT: B 905 GLU cc_start: 0.6939 (mp0) cc_final: 0.6194 (pm20) REVERT: B 911 GLU cc_start: 0.7393 (mt-10) cc_final: 0.7159 (mt-10) REVERT: B 947 LYS cc_start: 0.7845 (mtpt) cc_final: 0.7256 (mmtt) REVERT: B 1001 ARG cc_start: 0.5003 (OUTLIER) cc_final: 0.3198 (mpt-90) outliers start: 24 outliers final: 13 residues processed: 150 average time/residue: 1.4212 time to fit residues: 227.6213 Evaluate side-chains 154 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 HIS Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 1011 GLN Chi-restraints excluded: chain A residue 1016 THR Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 853 ARG Chi-restraints excluded: chain B residue 1001 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 83 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 115 optimal weight: 0.0060 chunk 99 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 79 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10186 Z= 0.177 Angle : 0.531 6.086 13867 Z= 0.278 Chirality : 0.041 0.210 1565 Planarity : 0.004 0.057 1741 Dihedral : 7.971 66.600 1465 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.67 % Favored : 96.25 % Rotamer: Outliers : 2.14 % Allowed : 24.22 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % 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: 1.21 (0.24), residues: 1252 helix: 2.04 (0.20), residues: 671 sheet: 0.35 (0.47), residues: 121 loop : -0.96 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 137 HIS 0.002 0.001 HIS B 761 PHE 0.024 0.001 PHE A 597 TYR 0.011 0.001 TYR A 626 ARG 0.013 0.001 ARG A1001 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 1.145 Fit side-chains REVERT: A 68 GLU cc_start: 0.7239 (mp0) cc_final: 0.6954 (mp0) REVERT: A 243 ASP cc_start: 0.6868 (m-30) cc_final: 0.6554 (m-30) REVERT: A 258 ASP cc_start: 0.7194 (OUTLIER) cc_final: 0.6462 (m-30) REVERT: A 331 ASP cc_start: 0.7449 (t0) cc_final: 0.7105 (t0) REVERT: A 336 ASP cc_start: 0.7031 (OUTLIER) cc_final: 0.6500 (t0) REVERT: A 345 ILE cc_start: 0.7437 (mt) cc_final: 0.7224 (mm) REVERT: A 406 ASP cc_start: 0.6442 (m-30) cc_final: 0.6190 (m-30) REVERT: A 416 GLU cc_start: 0.6298 (tm-30) cc_final: 0.5771 (tt0) REVERT: A 605 LYS cc_start: 0.7439 (tppp) cc_final: 0.7153 (tptt) REVERT: A 606 LYS cc_start: 0.6749 (mtmt) cc_final: 0.6434 (mttt) REVERT: A 718 ARG cc_start: 0.6954 (tpp80) cc_final: 0.6127 (mmp80) REVERT: A 776 ARG cc_start: 0.7060 (ptm160) cc_final: 0.6759 (ptp-110) REVERT: A 777 GLU cc_start: 0.7088 (mp0) cc_final: 0.6575 (pm20) REVERT: A 824 GLU cc_start: 0.6294 (mp0) cc_final: 0.5820 (mm-30) REVERT: A 827 LYS cc_start: 0.8170 (mmtm) cc_final: 0.7964 (mmtm) REVERT: A 853 ARG cc_start: 0.7363 (pmm150) cc_final: 0.6917 (mtm-85) REVERT: A 857 LYS cc_start: 0.7875 (mmmm) cc_final: 0.6963 (mmtt) REVERT: A 947 LYS cc_start: 0.7884 (mttp) cc_final: 0.7552 (mttp) REVERT: A 949 ARG cc_start: 0.6914 (tpp80) cc_final: 0.6497 (tpp-160) REVERT: A 967 ARG cc_start: 0.7879 (mtm-85) cc_final: 0.7549 (mmm-85) REVERT: A 999 ASP cc_start: 0.8172 (m-30) cc_final: 0.7891 (m-30) REVERT: A 1001 ARG cc_start: 0.8025 (ttm110) cc_final: 0.7571 (ttm110) REVERT: A 1011 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7571 (tp40) REVERT: B 667 ASN cc_start: 0.7275 (p0) cc_final: 0.6978 (m-40) REVERT: B 718 ARG cc_start: 0.6936 (mpp80) cc_final: 0.5965 (mmt180) REVERT: B 776 ARG cc_start: 0.7616 (mtm110) cc_final: 0.7256 (mmm-85) REVERT: B 827 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7200 (mmmt) REVERT: B 853 ARG cc_start: 0.7271 (OUTLIER) cc_final: 0.6870 (pmt170) REVERT: B 857 LYS cc_start: 0.7836 (mmtt) cc_final: 0.7620 (mmtm) REVERT: B 875 ARG cc_start: 0.6300 (ttp80) cc_final: 0.5278 (ttm110) REVERT: B 905 GLU cc_start: 0.6958 (mp0) cc_final: 0.6224 (pm20) REVERT: B 911 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7151 (mt-10) REVERT: B 947 LYS cc_start: 0.7932 (mtpt) cc_final: 0.7344 (mmtt) REVERT: B 1001 ARG cc_start: 0.4782 (OUTLIER) cc_final: 0.3130 (mpt-90) outliers start: 22 outliers final: 12 residues processed: 151 average time/residue: 1.3336 time to fit residues: 215.9480 Evaluate side-chains 156 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 HIS Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 1011 GLN Chi-restraints excluded: chain A residue 1016 THR Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 827 LYS Chi-restraints excluded: chain B residue 853 ARG Chi-restraints excluded: chain B residue 1001 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 4.9990 chunk 92 optimal weight: 0.0980 chunk 14 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.143787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.110776 restraints weight = 12120.236| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.92 r_work: 0.3210 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10186 Z= 0.217 Angle : 0.554 6.915 13867 Z= 0.289 Chirality : 0.042 0.211 1565 Planarity : 0.005 0.057 1741 Dihedral : 8.076 64.477 1464 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.99 % Favored : 95.93 % Rotamer: Outliers : 2.04 % Allowed : 24.42 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % 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: 1.15 (0.24), residues: 1252 helix: 1.98 (0.20), residues: 671 sheet: 0.37 (0.47), residues: 121 loop : -0.99 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 137 HIS 0.002 0.001 HIS B 890 PHE 0.023 0.001 PHE A 597 TYR 0.012 0.002 TYR A 626 ARG 0.013 0.001 ARG A1001 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4502.66 seconds wall clock time: 81 minutes 11.67 seconds (4871.67 seconds total)