Starting phenix.real_space_refine on Wed Jul 30 13:46:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mez_23808/07_2025/7mez_23808.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mez_23808/07_2025/7mez_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_23808/07_2025/7mez_23808.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mez_23808/07_2025/7mez_23808.map" model { file = "/net/cci-nas-00/data/ceres_data/7mez_23808/07_2025/7mez_23808.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mez_23808/07_2025/7mez_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 7.48, per 1000 atoms: 0.61 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: 2.79 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: 1.49 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: 4.50 Time building geometry restraints manager: 3.37 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: 1.860 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 30.740 Find NCS groups from input model: 0.120 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:13.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.910 ------------------------------------------------------------------------------- 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= 0.147 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 Details of bonding type rmsd hydrogen bonds : bond 0.11386 ( 617) hydrogen bonds : angle 5.32018 ( 1779) covalent geometry : bond 0.00326 (12639) covalent geometry : angle 0.56365 (17127) *********************** 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 : 1.284 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: 1.3343 time to fit residues: 229.4783 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 : 1.462 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.157399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.113699 restraints weight = 16507.894| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.36 r_work: 0.3259 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12639 Z= 0.178 Angle : 0.563 8.776 17127 Z= 0.290 Chirality : 0.043 0.163 1932 Planarity : 0.004 0.064 2179 Dihedral : 4.623 46.039 1658 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.57 % Favored : 96.23 % Rotamer: Outliers : 1.47 % Allowed : 7.69 % Favored : 90.84 % 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 Details of bonding type rmsd hydrogen bonds : bond 0.04031 ( 617) hydrogen bonds : angle 4.49376 ( 1779) covalent geometry : bond 0.00425 (12639) covalent geometry : angle 0.56330 (17127) *********************** 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 139 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 1.403 Fit side-chains REVERT: B 50 ARG cc_start: 0.7363 (ptp-170) cc_final: 0.6554 (tpp-160) REVERT: B 223 LEU cc_start: 0.7103 (OUTLIER) cc_final: 0.6835 (tm) REVERT: B 655 MET cc_start: 0.7463 (mmt) cc_final: 0.6671 (mtp) REVERT: B 744 MET cc_start: 0.7166 (mpp) cc_final: 0.6842 (mpp) REVERT: B 819 ASP cc_start: 0.5607 (m-30) cc_final: 0.5230 (m-30) outliers start: 20 outliers final: 8 residues processed: 130 average time/residue: 1.1984 time to fit residues: 171.1330 Evaluate side-chains 118 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 1.434 ------------------------------------------------------------------------------- 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 25 optimal weight: 0.9980 chunk 90 optimal weight: 0.0670 chunk 109 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 139 optimal weight: 9.9990 chunk 145 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.7518 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.158413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.114585 restraints weight = 16605.487| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.36 r_work: 0.3281 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12639 Z= 0.137 Angle : 0.518 7.669 17127 Z= 0.266 Chirality : 0.041 0.163 1932 Planarity : 0.004 0.066 2179 Dihedral : 4.365 32.968 1658 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.98 % Favored : 96.83 % Rotamer: Outliers : 1.98 % Allowed : 9.08 % Favored : 88.94 % 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: 0.73 (0.22), residues: 1512 helix: 1.59 (0.19), residues: 699 sheet: -0.32 (0.33), residues: 231 loop : -0.47 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 812 HIS 0.007 0.001 HIS B 607 PHE 0.013 0.001 PHE A 382 TYR 0.013 0.001 TYR A 720 ARG 0.009 0.000 ARG A 123 Details of bonding type rmsd hydrogen bonds : bond 0.03568 ( 617) hydrogen bonds : angle 4.31233 ( 1779) covalent geometry : bond 0.00322 (12639) covalent geometry : angle 0.51799 (17127) *********************** 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 152 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 1.276 Fit side-chains REVERT: A 772 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6748 (mp0) REVERT: A 903 LYS cc_start: 0.8398 (tptp) cc_final: 0.8160 (tptp) REVERT: B 50 ARG cc_start: 0.7544 (ptp-170) cc_final: 0.6501 (tpp-160) REVERT: B 223 LEU cc_start: 0.7175 (OUTLIER) cc_final: 0.6974 (tm) REVERT: B 251 GLN cc_start: 0.8393 (tp-100) cc_final: 0.8165 (tp-100) REVERT: B 655 MET cc_start: 0.7554 (mmt) cc_final: 0.6825 (mtp) outliers start: 27 outliers final: 13 residues processed: 141 average time/residue: 1.1499 time to fit residues: 178.4068 Evaluate side-chains 125 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 1.410 ------------------------------------------------------------------------------- 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 772 GLU 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 Chi-restraints excluded: chain B residue 223 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 38 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 144 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 137 optimal weight: 20.0000 chunk 145 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.155480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.107820 restraints weight = 16499.713| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.33 r_work: 0.3255 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12639 Z= 0.223 Angle : 0.581 7.501 17127 Z= 0.298 Chirality : 0.044 0.174 1932 Planarity : 0.004 0.066 2179 Dihedral : 4.459 28.092 1654 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.90 % Favored : 95.90 % Rotamer: Outliers : 2.05 % Allowed : 11.87 % Favored : 86.08 % 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: 0.51 (0.22), residues: 1512 helix: 1.46 (0.19), residues: 696 sheet: -0.60 (0.33), residues: 236 loop : -0.55 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 812 HIS 0.005 0.001 HIS B 607 PHE 0.017 0.002 PHE A 382 TYR 0.015 0.002 TYR B 109 ARG 0.009 0.000 ARG A 123 Details of bonding type rmsd hydrogen bonds : bond 0.04011 ( 617) hydrogen bonds : angle 4.40186 ( 1779) covalent geometry : bond 0.00536 (12639) covalent geometry : angle 0.58120 (17127) *********************** 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 143 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 1.341 Fit side-chains REVERT: A 772 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6722 (mp0) REVERT: A 1003 SER cc_start: 0.8039 (t) cc_final: 0.7495 (p) REVERT: B 50 ARG cc_start: 0.7581 (ptp-170) cc_final: 0.6549 (tpp-160) REVERT: B 223 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6864 (tm) REVERT: B 655 MET cc_start: 0.7541 (mmt) cc_final: 0.6726 (mtp) outliers start: 28 outliers final: 11 residues processed: 133 average time/residue: 1.1904 time to fit residues: 174.9363 Evaluate side-chains 124 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 1.519 ------------------------------------------------------------------------------- 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 772 GLU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 22 optimal weight: 0.3980 chunk 2 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.158468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.115076 restraints weight = 16214.546| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.22 r_work: 0.3295 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12639 Z= 0.130 Angle : 0.519 7.541 17127 Z= 0.266 Chirality : 0.041 0.163 1932 Planarity : 0.004 0.066 2179 Dihedral : 4.254 25.986 1654 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.51 % Favored : 96.36 % Rotamer: Outliers : 1.98 % Allowed : 12.89 % Favored : 85.13 % 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: 0.72 (0.22), residues: 1512 helix: 1.62 (0.19), residues: 698 sheet: -0.35 (0.33), residues: 233 loop : -0.49 (0.27), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 812 HIS 0.005 0.001 HIS B 607 PHE 0.012 0.001 PHE A 382 TYR 0.015 0.001 TYR A 720 ARG 0.008 0.000 ARG A 123 Details of bonding type rmsd hydrogen bonds : bond 0.03389 ( 617) hydrogen bonds : angle 4.24588 ( 1779) covalent geometry : bond 0.00306 (12639) covalent geometry : angle 0.51858 (17127) *********************** 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 154 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 1.563 Fit side-chains REVERT: A 772 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6776 (mp0) REVERT: A 903 LYS cc_start: 0.8380 (tptp) cc_final: 0.8159 (tptp) REVERT: B 50 ARG cc_start: 0.7673 (ptp-170) cc_final: 0.6695 (tpp-160) REVERT: B 223 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.7072 (tm) REVERT: B 655 MET cc_start: 0.7517 (mmt) cc_final: 0.6786 (mtp) outliers start: 27 outliers final: 15 residues processed: 142 average time/residue: 1.1857 time to fit residues: 186.1017 Evaluate side-chains 134 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 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 772 GLU 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 176 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 223 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 55 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 79 optimal weight: 0.0030 chunk 43 optimal weight: 0.9990 chunk 148 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.160431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.112377 restraints weight = 16532.327| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.41 r_work: 0.3371 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12639 Z= 0.140 Angle : 0.520 7.168 17127 Z= 0.265 Chirality : 0.041 0.167 1932 Planarity : 0.004 0.065 2179 Dihedral : 4.211 25.311 1654 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.77 % Favored : 96.10 % Rotamer: Outliers : 1.98 % Allowed : 13.85 % Favored : 84.18 % 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: 0.77 (0.22), residues: 1512 helix: 1.69 (0.19), residues: 697 sheet: -0.35 (0.33), residues: 233 loop : -0.50 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 252 HIS 0.005 0.001 HIS B 607 PHE 0.015 0.001 PHE A 175 TYR 0.015 0.001 TYR A 720 ARG 0.010 0.000 ARG A 123 Details of bonding type rmsd hydrogen bonds : bond 0.03405 ( 617) hydrogen bonds : angle 4.20727 ( 1779) covalent geometry : bond 0.00333 (12639) covalent geometry : angle 0.51978 (17127) *********************** 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 153 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 1.314 Fit side-chains REVERT: A 619 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8694 (pm20) REVERT: A 772 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6782 (mp0) REVERT: B 50 ARG cc_start: 0.7679 (ptp-170) cc_final: 0.6709 (tpp-160) REVERT: B 239 LEU cc_start: 0.8608 (tt) cc_final: 0.8391 (tp) REVERT: B 251 GLN cc_start: 0.8290 (tp-100) cc_final: 0.7992 (tp-100) REVERT: B 655 MET cc_start: 0.7518 (mmt) cc_final: 0.6854 (mtp) outliers start: 27 outliers final: 14 residues processed: 140 average time/residue: 1.1562 time to fit residues: 178.5538 Evaluate side-chains 134 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 1.389 ------------------------------------------------------------------------------- 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 619 GLN Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 876 ILE 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 606 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 47 optimal weight: 0.5980 chunk 3 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 50 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.160380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.114240 restraints weight = 16320.065| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.32 r_work: 0.3390 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1548 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= 0.130 Angle : 0.515 7.172 17127 Z= 0.263 Chirality : 0.041 0.164 1932 Planarity : 0.004 0.065 2179 Dihedral : 4.152 24.907 1654 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.70 % Favored : 96.16 % Rotamer: Outliers : 2.12 % Allowed : 14.36 % Favored : 83.52 % 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: 0.82 (0.22), residues: 1512 helix: 1.72 (0.19), residues: 697 sheet: -0.29 (0.34), residues: 226 loop : -0.48 (0.27), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP B 252 HIS 0.004 0.001 HIS B 607 PHE 0.012 0.001 PHE A 382 TYR 0.015 0.001 TYR A 720 ARG 0.011 0.000 ARG A 123 Details of bonding type rmsd hydrogen bonds : bond 0.03323 ( 617) hydrogen bonds : angle 4.17711 ( 1779) covalent geometry : bond 0.00307 (12639) covalent geometry : angle 0.51462 (17127) *********************** 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 155 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 1.341 Fit side-chains revert: symmetry clash REVERT: A 619 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8702 (pm20) REVERT: B 50 ARG cc_start: 0.7704 (ptp-170) cc_final: 0.6727 (tpp-160) REVERT: B 251 GLN cc_start: 0.8330 (tp-100) cc_final: 0.8125 (tp-100) REVERT: B 655 MET cc_start: 0.7517 (mmt) cc_final: 0.6865 (mtp) outliers start: 29 outliers final: 17 residues processed: 141 average time/residue: 1.1729 time to fit residues: 183.1981 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 : 1.389 ------------------------------------------------------------------------------- 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 551 LEU Chi-restraints excluded: chain A residue 619 GLN Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 890 LYS 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 764 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 112 optimal weight: 0.0970 chunk 132 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 118 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.161109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.115291 restraints weight = 16543.657| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.57 r_work: 0.3359 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12639 Z= 0.132 Angle : 0.522 7.097 17127 Z= 0.266 Chirality : 0.041 0.165 1932 Planarity : 0.004 0.064 2179 Dihedral : 4.132 24.720 1654 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.77 % Favored : 96.10 % Rotamer: Outliers : 2.34 % Allowed : 14.07 % 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 (0.34), residues: 233 loop : -0.49 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 252 HIS 0.011 0.001 HIS B 607 PHE 0.013 0.001 PHE A 175 TYR 0.015 0.001 TYR A 720 ARG 0.013 0.000 ARG A 123 Details of bonding type rmsd hydrogen bonds : bond 0.03289 ( 617) hydrogen bonds : angle 4.13574 ( 1779) covalent geometry : bond 0.00314 (12639) covalent geometry : angle 0.52152 (17127) *********************** 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 153 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 1.290 Fit side-chains revert: symmetry clash REVERT: A 139 GLN cc_start: 0.8675 (tt0) cc_final: 0.8374 (tt0) REVERT: A 146 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6931 (mp0) REVERT: A 982 ARG cc_start: 0.7251 (ttp-170) cc_final: 0.7003 (ttm170) REVERT: B 50 ARG cc_start: 0.7626 (ptp-170) cc_final: 0.6695 (tpp-160) REVERT: B 655 MET cc_start: 0.7398 (mmt) cc_final: 0.6759 (mtp) outliers start: 32 outliers final: 21 residues processed: 137 average time/residue: 1.1197 time to fit residues: 169.6069 Evaluate side-chains 140 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 1.422 ------------------------------------------------------------------------------- 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 551 LEU Chi-restraints excluded: chain A residue 823 LEU 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 606 SER Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 764 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 143 optimal weight: 0.7980 chunk 139 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 122 optimal weight: 8.9990 chunk 93 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 140 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.159874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.111560 restraints weight = 16415.534| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.42 r_work: 0.3361 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12639 Z= 0.176 Angle : 0.554 7.815 17127 Z= 0.283 Chirality : 0.042 0.170 1932 Planarity : 0.004 0.064 2179 Dihedral : 4.259 25.296 1654 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.84 % Favored : 96.03 % Rotamer: Outliers : 1.83 % Allowed : 15.16 % 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: 0.71 (0.22), residues: 1512 helix: 1.63 (0.19), residues: 695 sheet: -0.35 (0.34), residues: 226 loop : -0.54 (0.27), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 252 HIS 0.010 0.001 HIS B 607 PHE 0.016 0.001 PHE A 961 TYR 0.014 0.002 TYR A 720 ARG 0.014 0.000 ARG A 123 Details of bonding type rmsd hydrogen bonds : bond 0.03573 ( 617) hydrogen bonds : angle 4.20111 ( 1779) covalent geometry : bond 0.00425 (12639) covalent geometry : angle 0.55436 (17127) *********************** 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 146 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 1.473 Fit side-chains revert: symmetry clash REVERT: A 139 GLN cc_start: 0.8689 (tt0) cc_final: 0.8373 (tt0) REVERT: A 146 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7111 (mp0) REVERT: A 252 MET cc_start: 0.6206 (ppp) cc_final: 0.5953 (pp-130) REVERT: A 836 ASP cc_start: 0.7461 (t0) cc_final: 0.7231 (t0) REVERT: A 982 ARG cc_start: 0.7339 (ttp-170) cc_final: 0.7110 (ttm170) REVERT: B 50 ARG cc_start: 0.7657 (ptp-170) cc_final: 0.6691 (tpp-160) REVERT: B 251 GLN cc_start: 0.8194 (tp-100) cc_final: 0.7858 (tp-100) REVERT: B 619 ASN cc_start: 0.7884 (m-40) cc_final: 0.7352 (m110) REVERT: B 655 MET cc_start: 0.7486 (mmt) cc_final: 0.6816 (mtp) outliers start: 25 outliers final: 18 residues processed: 134 average time/residue: 1.1621 time to fit residues: 174.6425 Evaluate side-chains 135 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 1.446 ------------------------------------------------------------------------------- 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 823 LEU 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 961 PHE 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 178 VAL Chi-restraints excluded: chain B residue 606 SER Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 764 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 81 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.157807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.109420 restraints weight = 16460.490| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.41 r_work: 0.3330 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 12639 Z= 0.230 Angle : 0.604 8.342 17127 Z= 0.307 Chirality : 0.044 0.176 1932 Planarity : 0.004 0.064 2179 Dihedral : 4.472 26.338 1654 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.17 % Favored : 95.70 % Rotamer: Outliers : 1.54 % Allowed : 15.38 % Favored : 83.08 % 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: 0.44 (0.22), residues: 1512 helix: 1.43 (0.19), residues: 695 sheet: -0.59 (0.33), residues: 236 loop : -0.63 (0.27), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 252 HIS 0.010 0.001 HIS B 607 PHE 0.025 0.002 PHE A 961 TYR 0.013 0.002 TYR A 720 ARG 0.015 0.001 ARG A 123 Details of bonding type rmsd hydrogen bonds : bond 0.03973 ( 617) hydrogen bonds : angle 4.34952 ( 1779) covalent geometry : bond 0.00559 (12639) covalent geometry : angle 0.60382 (17127) ********************** 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 141 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 1.322 Fit side-chains REVERT: A 252 MET cc_start: 0.6196 (ppp) cc_final: 0.5976 (pp-130) REVERT: A 836 ASP cc_start: 0.7445 (t0) cc_final: 0.7233 (t0) REVERT: A 982 ARG cc_start: 0.7335 (ttp-170) cc_final: 0.7124 (ttm170) REVERT: B 50 ARG cc_start: 0.7711 (ptp-170) cc_final: 0.6706 (tpp-160) REVERT: B 223 LEU cc_start: 0.7181 (OUTLIER) cc_final: 0.6945 (tm) REVERT: B 251 GLN cc_start: 0.8168 (tp-100) cc_final: 0.7814 (tp-100) REVERT: B 619 ASN cc_start: 0.7972 (m-40) cc_final: 0.7415 (m110) REVERT: B 655 MET cc_start: 0.7538 (mmt) cc_final: 0.6870 (mtp) outliers start: 21 outliers final: 17 residues processed: 132 average time/residue: 1.3198 time to fit residues: 192.8153 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 : 1.352 ------------------------------------------------------------------------------- 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 497 PHE Chi-restraints excluded: chain A residue 823 LEU 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 961 PHE Chi-restraints excluded: chain A residue 1047 ASP Chi-restraints excluded: chain A residue 1074 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 223 LEU 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 148 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 136 optimal weight: 0.8980 chunk 147 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 100 optimal weight: 0.0770 chunk 95 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 overall best weight: 0.7138 ------------------------------------------------------------------------------- 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 775 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.159801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.111540 restraints weight = 16460.593| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.41 r_work: 0.3353 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12639 Z= 0.142 Angle : 0.562 7.769 17127 Z= 0.287 Chirality : 0.042 0.169 1932 Planarity : 0.004 0.063 2179 Dihedral : 4.372 25.573 1654 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.03 % Favored : 95.83 % Rotamer: Outliers : 1.83 % Allowed : 15.53 % Favored : 82.64 % 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: 0.64 (0.22), residues: 1512 helix: 1.59 (0.19), residues: 695 sheet: -0.45 (0.34), residues: 226 loop : -0.56 (0.27), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 252 HIS 0.010 0.001 HIS B 607 PHE 0.015 0.001 PHE A 961 TYR 0.016 0.001 TYR A 720 ARG 0.015 0.000 ARG A 123 Details of bonding type rmsd hydrogen bonds : bond 0.03518 ( 617) hydrogen bonds : angle 4.24655 ( 1779) covalent geometry : bond 0.00336 (12639) covalent geometry : angle 0.56222 (17127) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10056.15 seconds wall clock time: 176 minutes 41.11 seconds (10601.11 seconds total)