Starting phenix.real_space_refine on Mon Dec 30 06:23:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mez_23808/12_2024/7mez_23808.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mez_23808/12_2024/7mez_23808.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mez_23808/12_2024/7mez_23808.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mez_23808/12_2024/7mez_23808.map" model { file = "/net/cci-nas-00/data/ceres_data/7mez_23808/12_2024/7mez_23808.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mez_23808/12_2024/7mez_23808.cif" } resolution = 2.89 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= -0.002 sd= 0.135 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: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 7923 2.51 5 N 2130 2.21 5 O 2251 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 12361 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 989, 8046 Classifications: {'peptide': 989} Link IDs: {'PTRANS': 46, 'TRANS': 942} Chain breaks: 5 Chain: "B" Number of atoms: 4315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4315 Classifications: {'peptide': 547} Link IDs: {'PTRANS': 27, 'TRANS': 519} Chain breaks: 5 Time building chain proxies: 7.61, per 1000 atoms: 0.62 Number of scatterers: 12361 At special positions: 0 Unit cell: (90.015, 108.018, 149.319, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 2251 8.00 N 2130 7.00 C 7923 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.02 Conformation dependent library (CDL) restraints added in 1.6 seconds 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2920 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 12 sheets defined 50.4% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 69 through 82 Processing helix chain 'A' and resid 82 through 90 removed outlier: 4.082A pdb=" N ARG A 90 " --> pdb=" O ASP A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 117 Processing helix chain 'A' and resid 118 through 129 removed outlier: 3.654A pdb=" N LEU A 122 " --> pdb=" O THR A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 159 Processing helix chain 'A' and resid 171 through 180 Processing helix chain 'A' and resid 180 through 190 Processing helix chain 'A' and resid 192 through 199 Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 240 through 251 Processing helix chain 'A' and resid 286 through 289 Processing helix chain 'A' and resid 290 through 299 Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 355 through 357 No H-bonds generated for 'chain 'A' and resid 355 through 357' Processing helix chain 'A' and resid 421 through 423 No H-bonds generated for 'chain 'A' and resid 421 through 423' Processing helix chain 'A' and resid 498 through 503 removed outlier: 3.767A pdb=" N THR A 503 " --> pdb=" O ASP A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 561 Processing helix chain 'A' and resid 568 through 578 Processing helix chain 'A' and resid 578 through 583 Processing helix chain 'A' and resid 584 through 587 removed outlier: 6.593A pdb=" N LYS A 587 " --> pdb=" O LYS A 584 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 584 through 587' Processing helix chain 'A' and resid 588 through 595 Processing helix chain 'A' and resid 600 through 613 removed outlier: 3.815A pdb=" N ARG A 613 " --> pdb=" O GLN A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 631 Processing helix chain 'A' and resid 637 through 649 Processing helix chain 'A' and resid 652 through 667 removed outlier: 5.294A pdb=" N LEU A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N GLN A 662 " --> pdb=" O HIS A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 670 No H-bonds generated for 'chain 'A' and resid 668 through 670' Processing helix chain 'A' and resid 675 through 688 removed outlier: 3.562A pdb=" N ASN A 688 " --> pdb=" O ARG A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 706 removed outlier: 3.576A pdb=" N GLU A 702 " --> pdb=" O PHE A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 724 Processing helix chain 'A' and resid 725 through 752 removed outlier: 3.800A pdb=" N LEU A 752 " --> pdb=" O ASP A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 776 Processing helix chain 'A' and resid 798 through 801 Processing helix chain 'A' and resid 838 through 858 Processing helix chain 'A' and resid 888 through 896 removed outlier: 4.142A pdb=" N THR A 895 " --> pdb=" O ILE A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 914 Processing helix chain 'A' and resid 917 through 943 Processing helix chain 'A' and resid 948 through 950 No H-bonds generated for 'chain 'A' and resid 948 through 950' Processing helix chain 'A' and resid 964 through 976 removed outlier: 3.906A pdb=" N ILE A 968 " --> pdb=" O ASP A 964 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A 970 " --> pdb=" O GLY A 966 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN A 971 " --> pdb=" O HIS A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 996 Processing helix chain 'A' and resid 1003 through 1023 removed outlier: 3.643A pdb=" N HIS A1023 " --> pdb=" O ALA A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1039 removed outlier: 3.929A pdb=" N MET A1039 " --> pdb=" O LEU A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1055 Processing helix chain 'A' and resid 1060 through 1078 Processing helix chain 'A' and resid 1080 through 1091 Processing helix chain 'B' and resid 12 through 22 Processing helix chain 'B' and resid 42 through 49 removed outlier: 4.037A pdb=" N SER B 49 " --> pdb=" O GLN B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 73 removed outlier: 3.803A pdb=" N PHE B 55 " --> pdb=" O ASP B 51 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU B 56 " --> pdb=" O PRO B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 92 Processing helix chain 'B' and resid 100 through 111 Processing helix chain 'B' and resid 112 through 115 Processing helix chain 'B' and resid 116 through 136 removed outlier: 3.993A pdb=" N ILE B 122 " --> pdb=" O PRO B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 150 Processing helix chain 'B' and resid 172 through 184 Processing helix chain 'B' and resid 188 through 205 removed outlier: 3.845A pdb=" N THR B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 220 removed outlier: 3.953A pdb=" N SER B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 241 Processing helix chain 'B' and resid 245 through 265 Processing helix chain 'B' and resid 299 through 310 removed outlier: 3.772A pdb=" N GLU B 303 " --> pdb=" O ASP B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 524 No H-bonds generated for 'chain 'B' and resid 522 through 524' Processing helix chain 'B' and resid 525 through 540 Processing helix chain 'B' and resid 543 through 548 removed outlier: 3.675A pdb=" N THR B 547 " --> pdb=" O ARG B 543 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG B 548 " --> pdb=" O PRO B 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 543 through 548' Processing helix chain 'B' and resid 605 through 613 Processing helix chain 'B' and resid 613 through 620 Processing helix chain 'B' and resid 652 through 663 Processing helix chain 'B' and resid 696 through 707 Processing helix chain 'B' and resid 757 through 763 removed outlier: 3.753A pdb=" N GLN B 760 " --> pdb=" O CYS B 757 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N GLU B 761 " --> pdb=" O ARG B 758 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU B 762 " --> pdb=" O GLN B 759 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 58 removed outlier: 4.248A pdb=" N GLU A 55 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLU A 41 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N LEU A 137 " --> pdb=" O GLU A 41 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL A 43 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N GLN A 139 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N GLN A 134 " --> pdb=" O GLN A 101 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N GLN A 101 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 229 through 235 removed outlier: 4.390A pdb=" N ILE A 303 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU A 272 " --> pdb=" O LEU A 281 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 352 through 353 removed outlier: 6.112A pdb=" N VAL A 352 " --> pdb=" O ALA A 528 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 407 through 419 removed outlier: 7.547A pdb=" N VAL A 408 " --> pdb=" O ASP A 369 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ASP A 369 " --> pdb=" O VAL A 408 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N TRP A 410 " --> pdb=" O GLY A 367 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N GLY A 367 " --> pdb=" O TRP A 410 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE A 361 " --> pdb=" O PHE A 416 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N SER A 517 " --> pdb=" O ARG A 366 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE A 368 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N SER A 515 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 393 through 398 removed outlier: 6.501A pdb=" N LEU A 429 " --> pdb=" O ASN A 465 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ASN A 465 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU A 431 " --> pdb=" O TYR A 463 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TYR A 463 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE A 433 " --> pdb=" O LEU A 461 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 783 through 785 removed outlier: 5.804A pdb=" N LEU A 791 " --> pdb=" O VAL A 785 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N LYS A 816 " --> pdb=" O GLY A 794 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N LEU A 796 " --> pdb=" O GLU A 814 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N GLU A 814 " --> pdb=" O LEU A 796 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 783 through 785 removed outlier: 5.804A pdb=" N LEU A 791 " --> pdb=" O VAL A 785 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N LYS A 816 " --> pdb=" O GLY A 794 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N LEU A 796 " --> pdb=" O GLU A 814 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N GLU A 814 " --> pdb=" O LEU A 796 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE A 876 " --> pdb=" O THR A 872 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 885 through 887 Processing sheet with id=AA9, first strand: chain 'B' and resid 288 through 290 removed outlier: 8.400A pdb=" N TYR B 289 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL B 163 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N THR B 162 " --> pdb=" O ARG B 516 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL B 518 " --> pdb=" O THR B 162 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU B 164 " --> pdb=" O VAL B 518 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N PHE B 520 " --> pdb=" O LEU B 164 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU B 166 " --> pdb=" O PHE B 520 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 665 through 668 Processing sheet with id=AB2, first strand: chain 'B' and resid 683 through 689 removed outlier: 6.190A pdb=" N THR B 674 " --> pdb=" O GLU B 686 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N PHE B 688 " --> pdb=" O TYR B 672 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TYR B 672 " --> pdb=" O PHE B 688 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLN B 673 " --> pdb=" O VAL B 832 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL B 832 " --> pdb=" O GLN B 673 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLU B 675 " --> pdb=" O CYS B 830 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N CYS B 830 " --> pdb=" O GLU B 675 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N THR B 677 " --> pdb=" O ILE B 828 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS B 801 " --> pdb=" O SER B 731 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 795 through 799 621 hydrogen bonds defined for protein. 1779 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: 4.43 Time building geometry restraints manager: 3.51 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: 3968 1.34 - 1.46: 1699 1.46 - 1.57: 6891 1.57 - 1.69: 0 1.69 - 1.81: 81 Bond restraints: 12639 Sorted by residual: bond pdb=" N ASP A 111 " pdb=" CA ASP A 111 " ideal model delta sigma weight residual 1.457 1.502 -0.044 1.29e-02 6.01e+03 1.17e+01 bond pdb=" N ARG A 472 " pdb=" CA ARG A 472 " ideal model delta sigma weight residual 1.456 1.481 -0.025 1.18e-02 7.18e+03 4.64e+00 bond pdb=" N LEU B 305 " pdb=" CA LEU B 305 " ideal model delta sigma weight residual 1.459 1.480 -0.020 1.19e-02 7.06e+03 2.88e+00 bond pdb=" C ARG A 472 " pdb=" O ARG A 472 " ideal model delta sigma weight residual 1.236 1.218 0.018 1.28e-02 6.10e+03 1.90e+00 bond pdb=" C ILE B 304 " pdb=" N LEU B 305 " ideal model delta sigma weight residual 1.334 1.350 -0.015 1.27e-02 6.20e+03 1.44e+00 ... (remaining 12634 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 16905 2.14 - 4.27: 198 4.27 - 6.41: 18 6.41 - 8.55: 4 8.55 - 10.69: 2 Bond angle restraints: 17127 Sorted by residual: angle pdb=" N VAL B 269 " pdb=" CA VAL B 269 " pdb=" C VAL B 269 " ideal model delta sigma weight residual 113.47 108.17 5.30 1.01e+00 9.80e-01 2.76e+01 angle pdb=" N LYS A 112 " pdb=" CA LYS A 112 " pdb=" CB LYS A 112 " ideal model delta sigma weight residual 110.92 103.75 7.17 1.60e+00 3.91e-01 2.01e+01 angle pdb=" N GLY A 723 " pdb=" CA GLY A 723 " pdb=" C GLY A 723 " ideal model delta sigma weight residual 112.49 116.42 -3.93 1.21e+00 6.83e-01 1.05e+01 angle pdb=" N GLU A 772 " pdb=" CA GLU A 772 " pdb=" CB GLU A 772 " ideal model delta sigma weight residual 110.28 115.10 -4.82 1.55e+00 4.16e-01 9.67e+00 angle pdb=" CA LEU A 699 " pdb=" CB LEU A 699 " pdb=" CG LEU A 699 " ideal model delta sigma weight residual 116.30 126.99 -10.69 3.50e+00 8.16e-02 9.32e+00 ... (remaining 17122 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 6933 17.65 - 35.30: 579 35.30 - 52.95: 81 52.95 - 70.60: 16 70.60 - 88.25: 10 Dihedral angle restraints: 7619 sinusoidal: 3128 harmonic: 4491 Sorted by residual: dihedral pdb=" CA GLU A 68 " pdb=" C GLU A 68 " pdb=" N GLN A 69 " pdb=" CA GLN A 69 " ideal model delta harmonic sigma weight residual 180.00 150.75 29.25 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA HIS B 94 " pdb=" C HIS B 94 " pdb=" N PHE B 95 " pdb=" CA PHE B 95 " ideal model delta harmonic sigma weight residual 180.00 161.25 18.75 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA VAL A 67 " pdb=" C VAL A 67 " pdb=" N GLU A 68 " pdb=" CA GLU A 68 " ideal model delta harmonic sigma weight residual 180.00 162.26 17.74 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 7616 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1366 0.039 - 0.078: 403 0.078 - 0.116: 141 0.116 - 0.155: 20 0.155 - 0.194: 2 Chirality restraints: 1932 Sorted by residual: chirality pdb=" CB ILE A 368 " pdb=" CA ILE A 368 " pdb=" CG1 ILE A 368 " pdb=" CG2 ILE A 368 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.42e-01 chirality pdb=" CA ILE B 729 " pdb=" N ILE B 729 " pdb=" C ILE B 729 " pdb=" CB ILE B 729 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.77e-01 chirality pdb=" CA THR A 182 " pdb=" N THR A 182 " pdb=" C THR A 182 " pdb=" CB THR A 182 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.86e-01 ... (remaining 1929 not shown) Planarity restraints: 2179 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 304 " 0.020 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" C ILE B 304 " -0.067 2.00e-02 2.50e+03 pdb=" O ILE B 304 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU B 305 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 988 " -0.039 5.00e-02 4.00e+02 5.83e-02 5.43e+00 pdb=" N PRO A 989 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 989 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 989 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 274 " -0.032 5.00e-02 4.00e+02 4.81e-02 3.71e+00 pdb=" N PRO B 275 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 275 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 275 " -0.027 5.00e-02 4.00e+02 ... (remaining 2176 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 612 2.73 - 3.27: 12420 3.27 - 3.81: 20558 3.81 - 4.36: 24737 4.36 - 4.90: 42796 Nonbonded interactions: 101123 Sorted by model distance: nonbonded pdb=" OG SER B 754 " pdb=" OG1 THR B 771 " model vdw 2.187 3.040 nonbonded pdb=" OG SER B 691 " pdb=" OD1 ASP B 817 " model vdw 2.201 3.040 nonbonded pdb=" OG1 THR A 333 " pdb=" O LEU A 529 " model vdw 2.224 3.040 nonbonded pdb=" NH1 ARG B 537 " pdb=" O LEU B 865 " model vdw 2.239 3.120 nonbonded pdb=" NH1 ARG B 531 " pdb=" O PHE B 688 " model vdw 2.240 3.120 ... (remaining 101118 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: 2.370 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: 0.510 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 30.930 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 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 : 0.003 0.044 12639 Z= 0.213 Angle : 0.564 10.685 17127 Z= 0.297 Chirality : 0.042 0.194 1932 Planarity : 0.004 0.058 2179 Dihedral : 13.142 88.251 4699 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.31 % Favored : 96.49 % Rotamer: Outliers : 0.07 % Allowed : 0.00 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.22), residues: 1512 helix: 1.47 (0.20), residues: 687 sheet: -0.35 (0.33), residues: 234 loop : -0.46 (0.27), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 812 HIS 0.010 0.001 HIS A 346 PHE 0.015 0.001 PHE B 298 TYR 0.017 0.001 TYR B 730 ARG 0.007 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 1.440 Fit side-chains REVERT: B 655 MET cc_start: 0.7120 (mmt) cc_final: 0.6321 (mtp) outliers start: 1 outliers final: 1 residues processed: 158 average time/residue: 1.3915 time to fit residues: 239.3474 Evaluate side-chains 111 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 138 optimal weight: 0.6980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN ** A 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1060 ASN ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12639 Z= 0.279 Angle : 0.564 8.851 17127 Z= 0.290 Chirality : 0.043 0.163 1932 Planarity : 0.004 0.065 2179 Dihedral : 4.629 46.426 1658 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.57 % Favored : 96.23 % Rotamer: Outliers : 1.54 % Allowed : 7.55 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.59 (0.22), residues: 1512 helix: 1.47 (0.19), residues: 697 sheet: -0.43 (0.32), residues: 241 loop : -0.49 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 812 HIS 0.009 0.001 HIS B 607 PHE 0.014 0.001 PHE A 382 TYR 0.017 0.002 TYR B 730 ARG 0.008 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 1.594 Fit side-chains REVERT: B 50 ARG cc_start: 0.7277 (ptp-170) cc_final: 0.6661 (tpp-160) REVERT: B 223 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6959 (tm) REVERT: B 655 MET cc_start: 0.7066 (mmt) cc_final: 0.6404 (mtp) REVERT: B 744 MET cc_start: 0.7237 (mpp) cc_final: 0.6916 (mpp) outliers start: 21 outliers final: 8 residues processed: 131 average time/residue: 1.2456 time to fit residues: 178.8644 Evaluate side-chains 117 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 346 HIS Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain A residue 472 ARG Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 1047 ASP Chi-restraints excluded: chain B residue 223 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 38 optimal weight: 0.3980 chunk 138 optimal weight: 0.9990 chunk 149 optimal weight: 0.0970 chunk 123 optimal weight: 0.0040 chunk 137 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 773 ASN ** A 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1060 ASN ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12639 Z= 0.164 Angle : 0.501 7.806 17127 Z= 0.257 Chirality : 0.041 0.157 1932 Planarity : 0.004 0.065 2179 Dihedral : 4.271 32.086 1658 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.84 % Favored : 96.96 % Rotamer: Outliers : 1.83 % Allowed : 9.45 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.22), residues: 1512 helix: 1.71 (0.19), residues: 698 sheet: -0.24 (0.33), residues: 231 loop : -0.44 (0.27), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 812 HIS 0.007 0.001 HIS B 607 PHE 0.011 0.001 PHE A 382 TYR 0.014 0.001 TYR A 720 ARG 0.009 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 1.465 Fit side-chains REVERT: A 619 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8336 (pm20) REVERT: B 50 ARG cc_start: 0.7524 (ptp-170) cc_final: 0.6727 (tpp-160) REVERT: B 655 MET cc_start: 0.6979 (mmt) cc_final: 0.6408 (mtp) outliers start: 25 outliers final: 10 residues processed: 141 average time/residue: 1.1398 time to fit residues: 178.0217 Evaluate side-chains 126 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 346 HIS Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 619 GLN Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 176 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 71 optimal weight: 0.0040 chunk 15 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 146 optimal weight: 0.0870 chunk 72 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.9374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 773 ASN ** A 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1060 ASN ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12639 Z= 0.244 Angle : 0.524 7.345 17127 Z= 0.269 Chirality : 0.042 0.165 1932 Planarity : 0.004 0.064 2179 Dihedral : 4.197 26.918 1654 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.44 % Favored : 96.36 % Rotamer: Outliers : 1.54 % Allowed : 11.94 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.22), residues: 1512 helix: 1.69 (0.19), residues: 698 sheet: -0.28 (0.33), residues: 231 loop : -0.46 (0.27), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 812 HIS 0.006 0.001 HIS B 607 PHE 0.014 0.001 PHE A 382 TYR 0.019 0.001 TYR B 730 ARG 0.008 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 1.501 Fit side-chains REVERT: B 50 ARG cc_start: 0.7520 (ptp-170) cc_final: 0.6713 (tpp-160) REVERT: B 655 MET cc_start: 0.7040 (mmt) cc_final: 0.6430 (mtp) outliers start: 21 outliers final: 12 residues processed: 137 average time/residue: 1.2174 time to fit residues: 183.7587 Evaluate side-chains 128 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 346 HIS Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 890 LYS Chi-restraints excluded: chain A residue 1047 ASP Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 176 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 0.0570 chunk 83 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1060 ASN ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12639 Z= 0.318 Angle : 0.563 6.933 17127 Z= 0.288 Chirality : 0.043 0.172 1932 Planarity : 0.004 0.066 2179 Dihedral : 4.342 26.282 1654 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.84 % Favored : 96.03 % Rotamer: Outliers : 2.12 % Allowed : 12.60 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.22), residues: 1512 helix: 1.56 (0.19), residues: 695 sheet: -0.50 (0.34), residues: 226 loop : -0.54 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 812 HIS 0.005 0.001 HIS B 607 PHE 0.017 0.001 PHE A 382 TYR 0.014 0.002 TYR A 720 ARG 0.008 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 1.670 Fit side-chains REVERT: B 50 ARG cc_start: 0.7569 (ptp-170) cc_final: 0.6794 (tpp-160) REVERT: B 223 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.7084 (tm) REVERT: B 655 MET cc_start: 0.7067 (mmt) cc_final: 0.6473 (mtp) outliers start: 29 outliers final: 13 residues processed: 137 average time/residue: 1.1933 time to fit residues: 180.3335 Evaluate side-chains 129 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 346 HIS Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 1047 ASP Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 606 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 86 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 chunk 147 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 68 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 GLN ** A 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1060 ASN ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12639 Z= 0.252 Angle : 0.538 7.019 17127 Z= 0.275 Chirality : 0.042 0.167 1932 Planarity : 0.004 0.066 2179 Dihedral : 4.280 25.655 1654 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.64 % Favored : 96.23 % Rotamer: Outliers : 1.90 % Allowed : 13.77 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.22), residues: 1512 helix: 1.59 (0.19), residues: 695 sheet: -0.42 (0.34), residues: 226 loop : -0.50 (0.27), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 252 HIS 0.005 0.001 HIS B 607 PHE 0.014 0.001 PHE A 175 TYR 0.014 0.001 TYR A 720 ARG 0.010 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 1.521 Fit side-chains REVERT: B 50 ARG cc_start: 0.7600 (ptp-170) cc_final: 0.6863 (tpp-160) REVERT: B 223 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.7097 (tm) REVERT: B 655 MET cc_start: 0.7036 (mmt) cc_final: 0.6488 (mtp) outliers start: 26 outliers final: 17 residues processed: 137 average time/residue: 1.1920 time to fit residues: 180.2175 Evaluate side-chains 135 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 346 HIS Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 890 LYS Chi-restraints excluded: chain A residue 1047 ASP Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 606 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 123 optimal weight: 0.4980 chunk 82 optimal weight: 0.7980 chunk 146 optimal weight: 20.0000 chunk 91 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 67 optimal weight: 0.0020 chunk 90 optimal weight: 0.3980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1060 ASN ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12639 Z= 0.179 Angle : 0.506 7.016 17127 Z= 0.258 Chirality : 0.041 0.161 1932 Planarity : 0.004 0.065 2179 Dihedral : 4.120 24.477 1654 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.44 % Favored : 96.43 % Rotamer: Outliers : 1.98 % Allowed : 13.99 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.22), residues: 1512 helix: 1.74 (0.19), residues: 697 sheet: -0.28 (0.34), residues: 233 loop : -0.46 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 252 HIS 0.004 0.001 HIS B 607 PHE 0.011 0.001 PHE A 175 TYR 0.015 0.001 TYR A 720 ARG 0.012 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 1.563 Fit side-chains REVERT: B 50 ARG cc_start: 0.7568 (ptp-170) cc_final: 0.6838 (tpp-160) REVERT: B 252 TRP cc_start: 0.7572 (t60) cc_final: 0.7362 (t60) REVERT: B 655 MET cc_start: 0.6968 (mmt) cc_final: 0.6492 (mtp) outliers start: 27 outliers final: 14 residues processed: 145 average time/residue: 1.1951 time to fit residues: 190.8470 Evaluate side-chains 132 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 346 HIS Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain A residue 1047 ASP Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 606 SER Chi-restraints excluded: chain B residue 656 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 44 optimal weight: 0.4980 chunk 28 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 72 optimal weight: 0.4980 chunk 13 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 chunk 140 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 773 ASN A 893 GLN ** A 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1060 ASN ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12639 Z= 0.217 Angle : 0.529 8.197 17127 Z= 0.270 Chirality : 0.041 0.162 1932 Planarity : 0.004 0.063 2179 Dihedral : 4.142 24.708 1654 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.77 % Favored : 96.10 % Rotamer: Outliers : 1.98 % Allowed : 14.43 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.22), residues: 1512 helix: 1.74 (0.19), residues: 697 sheet: -0.28 (0.33), residues: 233 loop : -0.49 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 252 HIS 0.011 0.001 HIS B 607 PHE 0.013 0.001 PHE A 175 TYR 0.014 0.001 TYR A 720 ARG 0.012 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 1.534 Fit side-chains REVERT: B 50 ARG cc_start: 0.7553 (ptp-170) cc_final: 0.6851 (tpp-160) REVERT: B 655 MET cc_start: 0.6987 (mmt) cc_final: 0.6501 (mtp) outliers start: 27 outliers final: 15 residues processed: 133 average time/residue: 1.2422 time to fit residues: 182.2379 Evaluate side-chains 129 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 346 HIS Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 890 LYS Chi-restraints excluded: chain A residue 1047 ASP Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 606 SER Chi-restraints excluded: chain B residue 700 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.7980 chunk 136 optimal weight: 0.9990 chunk 140 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 129 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 144 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1060 ASN ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12639 Z= 0.225 Angle : 0.540 7.230 17127 Z= 0.275 Chirality : 0.041 0.164 1932 Planarity : 0.004 0.063 2179 Dihedral : 4.169 24.645 1654 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.70 % Favored : 96.16 % Rotamer: Outliers : 1.68 % Allowed : 15.46 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.22), residues: 1512 helix: 1.71 (0.19), residues: 697 sheet: -0.28 (0.34), residues: 233 loop : -0.49 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 252 HIS 0.010 0.001 HIS B 607 PHE 0.013 0.001 PHE A 382 TYR 0.014 0.001 TYR A 720 ARG 0.014 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 1.481 Fit side-chains REVERT: A 146 GLU cc_start: 0.6687 (OUTLIER) cc_final: 0.6435 (mp0) REVERT: B 50 ARG cc_start: 0.7525 (ptp-170) cc_final: 0.6817 (tpp-160) REVERT: B 655 MET cc_start: 0.6960 (mmt) cc_final: 0.6472 (mtp) outliers start: 23 outliers final: 17 residues processed: 133 average time/residue: 1.1539 time to fit residues: 169.6113 Evaluate side-chains 134 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 346 HIS Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 890 LYS Chi-restraints excluded: chain A residue 1047 ASP Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 606 SER Chi-restraints excluded: chain B residue 700 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.7980 chunk 68 optimal weight: 0.5980 chunk 100 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 139 optimal weight: 0.0980 chunk 120 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1060 ASN ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12639 Z= 0.209 Angle : 0.535 7.919 17127 Z= 0.273 Chirality : 0.041 0.163 1932 Planarity : 0.004 0.063 2179 Dihedral : 4.146 24.378 1654 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.77 % Favored : 96.10 % Rotamer: Outliers : 1.47 % Allowed : 15.53 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.22), residues: 1512 helix: 1.74 (0.19), residues: 698 sheet: -0.23 (0.33), residues: 238 loop : -0.48 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 252 HIS 0.010 0.001 HIS B 607 PHE 0.012 0.001 PHE A 382 TYR 0.015 0.001 TYR A 720 ARG 0.014 0.000 ARG A 123 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3024 Ramachandran restraints generated. 1512 Oldfield, 0 Emsley, 1512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 1.529 Fit side-chains REVERT: A 146 GLU cc_start: 0.6670 (OUTLIER) cc_final: 0.6417 (mp0) REVERT: B 50 ARG cc_start: 0.7517 (ptp-170) cc_final: 0.6809 (tpp-160) REVERT: B 655 MET cc_start: 0.6952 (mmt) cc_final: 0.6484 (mtp) outliers start: 20 outliers final: 16 residues processed: 135 average time/residue: 1.2142 time to fit residues: 181.2350 Evaluate side-chains 132 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 346 HIS Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 890 LYS Chi-restraints excluded: chain A residue 1047 ASP Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 606 SER Chi-restraints excluded: chain B residue 700 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 0.7980 chunk 111 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1060 ASN ** B 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.160638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.113118 restraints weight = 16285.524| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.38 r_work: 0.3381 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12639 Z= 0.225 Angle : 0.543 7.799 17127 Z= 0.277 Chirality : 0.041 0.163 1932 Planarity : 0.004 0.063 2179 Dihedral : 4.171 24.468 1654 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.77 % Favored : 96.10 % Rotamer: Outliers : 1.54 % Allowed : 15.68 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.22), residues: 1512 helix: 1.73 (0.19), residues: 698 sheet: -0.31 (0.33), residues: 233 loop : -0.50 (0.27), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 252 HIS 0.010 0.001 HIS B 607 PHE 0.013 0.001 PHE A 961 TYR 0.014 0.001 TYR A 720 ARG 0.015 0.000 ARG A 123 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4018.44 seconds wall clock time: 73 minutes 20.56 seconds (4400.56 seconds total)