Starting phenix.real_space_refine on Fri Jan 17 02:22:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cxj_45993/01_2025/9cxj_45993.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cxj_45993/01_2025/9cxj_45993.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cxj_45993/01_2025/9cxj_45993.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cxj_45993/01_2025/9cxj_45993.map" model { file = "/net/cci-nas-00/data/ceres_data/9cxj_45993/01_2025/9cxj_45993.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cxj_45993/01_2025/9cxj_45993.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 Mg 2 5.21 5 S 64 5.16 5 C 6573 2.51 5 N 1695 2.21 5 O 1891 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 10227 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4909 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 24, 'TRANS': 570} Chain: "B" Number of atoms: 4893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4893 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 24, 'TRANS': 568} Chain: "C" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 205 Classifications: {'peptide': 24} Modifications used: {'COO': 1} Link IDs: {'TRANS': 23} Chain breaks: 1 Chain: "D" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 216 Classifications: {'peptide': 25} Modifications used: {'COO': 1} Link IDs: {'TRANS': 24} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.79, per 1000 atoms: 0.66 Number of scatterers: 10227 At special positions: 0 Unit cell: (106.683, 116.607, 104.202, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 64 16.00 Mg 2 11.99 O 1891 8.00 N 1695 7.00 C 6573 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: 2.75 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 566 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 602 " pdb=" ZN B 901 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 602 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 566 " 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2378 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 2 sheets defined 66.5% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 231 through 251 Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 289 through 298 Proline residue: A 295 - end of helix Processing helix chain 'A' and resid 347 through 356 Processing helix chain 'A' and resid 415 through 461 removed outlier: 4.459A pdb=" N LEU A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASN A 435 " --> pdb=" O TRP A 431 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR A 436 " --> pdb=" O SER A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 471 removed outlier: 3.764A pdb=" N ILE A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 478 removed outlier: 3.694A pdb=" N LYS A 476 " --> pdb=" O LYS A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 498 removed outlier: 3.521A pdb=" N LEU A 490 " --> pdb=" O GLU A 486 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP A 497 " --> pdb=" O ILE A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 532 removed outlier: 3.529A pdb=" N ILE A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 556 removed outlier: 3.618A pdb=" N TYR A 556 " --> pdb=" O VAL A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 580 Processing helix chain 'A' and resid 582 through 587 removed outlier: 3.758A pdb=" N LYS A 585 " --> pdb=" O ARG A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 600 removed outlier: 4.197A pdb=" N ALA A 594 " --> pdb=" O LEU A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 618 Processing helix chain 'A' and resid 619 through 625 Processing helix chain 'A' and resid 628 through 644 removed outlier: 3.867A pdb=" N ASP A 644 " --> pdb=" O THR A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 670 Processing helix chain 'A' and resid 673 through 693 removed outlier: 3.560A pdb=" N TYR A 677 " --> pdb=" O ASP A 673 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N THR A 682 " --> pdb=" O PHE A 678 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N MET A 683 " --> pdb=" O LYS A 679 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN A 693 " --> pdb=" O ASP A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 707 removed outlier: 4.202A pdb=" N ASP A 707 " --> pdb=" O TYR A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 724 removed outlier: 3.653A pdb=" N LYS A 711 " --> pdb=" O ASP A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 729 Processing helix chain 'A' and resid 730 through 756 Processing helix chain 'A' and resid 765 through 770 removed outlier: 4.749A pdb=" N ASP A 770 " --> pdb=" O ASN A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 783 Processing helix chain 'A' and resid 783 through 795 removed outlier: 4.289A pdb=" N VAL A 787 " --> pdb=" O VAL A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 825 removed outlier: 3.733A pdb=" N LEU A 802 " --> pdb=" O ILE A 798 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 251 Processing helix chain 'B' and resid 256 through 268 Processing helix chain 'B' and resid 268 through 273 removed outlier: 3.974A pdb=" N ASN B 273 " --> pdb=" O ARG B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 298 Proline residue: B 295 - end of helix Processing helix chain 'B' and resid 341 through 346 removed outlier: 4.362A pdb=" N SER B 346 " --> pdb=" O TRP B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 356 Processing helix chain 'B' and resid 364 through 367 Processing helix chain 'B' and resid 415 through 461 removed outlier: 4.433A pdb=" N LEU B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASN B 435 " --> pdb=" O TRP B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 469 Processing helix chain 'B' and resid 472 through 478 Processing helix chain 'B' and resid 486 through 496 removed outlier: 3.542A pdb=" N GLU B 496 " --> pdb=" O ALA B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 4.028A pdb=" N GLU B 505 " --> pdb=" O ARG B 502 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU B 506 " --> pdb=" O SER B 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 502 through 506' Processing helix chain 'B' and resid 517 through 532 removed outlier: 3.538A pdb=" N ILE B 532 " --> pdb=" O LEU B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 556 Processing helix chain 'B' and resid 563 through 580 Processing helix chain 'B' and resid 582 through 587 removed outlier: 3.551A pdb=" N LYS B 585 " --> pdb=" O ARG B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 601 removed outlier: 3.581A pdb=" N CYS B 601 " --> pdb=" O ALA B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 618 Processing helix chain 'B' and resid 619 through 625 Processing helix chain 'B' and resid 628 through 644 removed outlier: 3.630A pdb=" N ASP B 644 " --> pdb=" O THR B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 671 Processing helix chain 'B' and resid 673 through 692 removed outlier: 5.016A pdb=" N THR B 682 " --> pdb=" O PHE B 678 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N MET B 683 " --> pdb=" O LYS B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 707 removed outlier: 4.178A pdb=" N ASP B 707 " --> pdb=" O TYR B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 724 removed outlier: 3.792A pdb=" N LYS B 711 " --> pdb=" O ASP B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 729 Processing helix chain 'B' and resid 730 through 757 removed outlier: 3.747A pdb=" N GLN B 736 " --> pdb=" O GLU B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 765 through 770 removed outlier: 5.116A pdb=" N ASP B 770 " --> pdb=" O ASN B 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 783 Processing helix chain 'B' and resid 783 through 795 removed outlier: 4.161A pdb=" N VAL B 787 " --> pdb=" O VAL B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 823 removed outlier: 3.768A pdb=" N LEU B 802 " --> pdb=" O ILE B 798 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU B 818 " --> pdb=" O SER B 814 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR B 819 " --> pdb=" O LEU B 815 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 84 removed outlier: 4.497A pdb=" N ALA C 82 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLN C 83 " --> pdb=" O HIS C 79 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 84 removed outlier: 4.327A pdb=" N HIS D 79 " --> pdb=" O HIS D 75 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU D 80 " --> pdb=" O LEU D 76 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 330 through 335 removed outlier: 3.708A pdb=" N LYS A 319 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR A 277 " --> pdb=" O TYR A 323 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL A 400 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY A 401 " --> pdb=" O ILE A 392 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 330 through 335 removed outlier: 3.741A pdb=" N LYS B 319 " --> pdb=" O LEU B 281 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR B 277 " --> pdb=" O TYR B 323 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL B 400 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY B 401 " --> pdb=" O ILE B 392 " (cutoff:3.500A) 601 hydrogen bonds defined for protein. 1746 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.07 Time building geometry restraints manager: 3.16 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: 3251 1.34 - 1.46: 1557 1.46 - 1.57: 5541 1.57 - 1.69: 0 1.69 - 1.81: 112 Bond restraints: 10461 Sorted by residual: bond pdb=" CB VAL B 787 " pdb=" CG2 VAL B 787 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.29e+00 bond pdb=" CA THR B 618 " pdb=" CB THR B 618 " ideal model delta sigma weight residual 1.530 1.552 -0.022 1.50e-02 4.44e+03 2.14e+00 bond pdb=" CA THR A 618 " pdb=" CB THR A 618 " ideal model delta sigma weight residual 1.530 1.550 -0.021 1.50e-02 4.44e+03 1.87e+00 bond pdb=" C LEU A 590 " pdb=" N GLU A 591 " ideal model delta sigma weight residual 1.333 1.315 0.018 1.38e-02 5.25e+03 1.69e+00 bond pdb=" CG LYS B 249 " pdb=" CD LYS B 249 " ideal model delta sigma weight residual 1.520 1.483 0.037 3.00e-02 1.11e+03 1.48e+00 ... (remaining 10456 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 13436 1.54 - 3.08: 587 3.08 - 4.63: 71 4.63 - 6.17: 33 6.17 - 7.71: 4 Bond angle restraints: 14131 Sorted by residual: angle pdb=" CA THR A 618 " pdb=" CB THR A 618 " pdb=" CG2 THR A 618 " ideal model delta sigma weight residual 110.50 116.59 -6.09 1.70e+00 3.46e-01 1.28e+01 angle pdb=" N GLU A 591 " pdb=" CA GLU A 591 " pdb=" C GLU A 591 " ideal model delta sigma weight residual 113.88 109.53 4.35 1.23e+00 6.61e-01 1.25e+01 angle pdb=" CA THR B 618 " pdb=" CB THR B 618 " pdb=" CG2 THR B 618 " ideal model delta sigma weight residual 110.50 116.29 -5.79 1.70e+00 3.46e-01 1.16e+01 angle pdb=" N ASP B 750 " pdb=" CA ASP B 750 " pdb=" C ASP B 750 " ideal model delta sigma weight residual 111.28 107.96 3.32 1.09e+00 8.42e-01 9.26e+00 angle pdb=" C SER A 617 " pdb=" N THR A 618 " pdb=" CA THR A 618 " ideal model delta sigma weight residual 122.19 126.42 -4.23 1.41e+00 5.03e-01 8.98e+00 ... (remaining 14126 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.97: 5695 16.97 - 33.93: 451 33.93 - 50.90: 118 50.90 - 67.87: 48 67.87 - 84.83: 15 Dihedral angle restraints: 6327 sinusoidal: 2664 harmonic: 3663 Sorted by residual: dihedral pdb=" CA ARG A 276 " pdb=" C ARG A 276 " pdb=" N TYR A 277 " pdb=" CA TYR A 277 " ideal model delta harmonic sigma weight residual 180.00 160.27 19.73 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA VAL B 783 " pdb=" C VAL B 783 " pdb=" N CYS B 784 " pdb=" CA CYS B 784 " ideal model delta harmonic sigma weight residual -180.00 -160.55 -19.45 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA SER A 628 " pdb=" C SER A 628 " pdb=" N ILE A 629 " pdb=" CA ILE A 629 " ideal model delta harmonic sigma weight residual 180.00 -161.02 -18.98 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 6324 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 975 0.042 - 0.083: 399 0.083 - 0.125: 143 0.125 - 0.166: 11 0.166 - 0.208: 8 Chirality restraints: 1536 Sorted by residual: chirality pdb=" CA THR B 618 " pdb=" N THR B 618 " pdb=" C THR B 618 " pdb=" CB THR B 618 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA THR A 618 " pdb=" N THR A 618 " pdb=" C THR A 618 " pdb=" CB THR A 618 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA ILE A 392 " pdb=" N ILE A 392 " pdb=" C ILE A 392 " pdb=" CB ILE A 392 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.94e-01 ... (remaining 1533 not shown) Planarity restraints: 1802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 507 " 0.009 2.00e-02 2.50e+03 2.60e-02 1.36e+01 pdb=" CG TYR B 507 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR B 507 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR B 507 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 507 " -0.035 2.00e-02 2.50e+03 pdb=" CE2 TYR B 507 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 507 " -0.036 2.00e-02 2.50e+03 pdb=" OH TYR B 507 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 84 " 0.009 2.00e-02 2.50e+03 2.59e-02 1.34e+01 pdb=" CG TYR D 84 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR D 84 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR D 84 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 TYR D 84 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR D 84 " 0.036 2.00e-02 2.50e+03 pdb=" CZ TYR D 84 " 0.037 2.00e-02 2.50e+03 pdb=" OH TYR D 84 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 589 " -0.018 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C ASP A 589 " 0.061 2.00e-02 2.50e+03 pdb=" O ASP A 589 " -0.023 2.00e-02 2.50e+03 pdb=" N LEU A 590 " -0.021 2.00e-02 2.50e+03 ... (remaining 1799 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 61 2.56 - 3.14: 8346 3.14 - 3.73: 16321 3.73 - 4.31: 22568 4.31 - 4.90: 38023 Nonbonded interactions: 85319 Sorted by model distance: nonbonded pdb=" OD1 ASP B 723 " pdb="ZN ZN B 901 " model vdw 1.970 2.230 nonbonded pdb=" OD2 ASP A 603 " pdb="ZN ZN A 901 " model vdw 1.987 2.230 nonbonded pdb=" OD1 ASP A 723 " pdb="ZN ZN A 901 " model vdw 1.990 2.230 nonbonded pdb=" OD2 ASP B 603 " pdb="ZN ZN B 901 " model vdw 1.993 2.230 nonbonded pdb=" OD2 ASP B 723 " pdb="ZN ZN B 901 " model vdw 2.038 2.230 ... (remaining 85314 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 231 through 823 or resid 901 through 902)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 28 through 35 or resid 72 through 87)) } 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: 2.040 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: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 27.930 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10461 Z= 0.243 Angle : 0.751 7.708 14131 Z= 0.439 Chirality : 0.050 0.208 1536 Planarity : 0.009 0.087 1802 Dihedral : 14.796 84.834 3949 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.42 % Allowed : 7.64 % Favored : 90.93 % 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: -0.11 (0.23), residues: 1225 helix: 0.15 (0.17), residues: 740 sheet: -1.15 (0.53), residues: 80 loop : 0.06 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 746 HIS 0.007 0.001 HIS A 634 PHE 0.023 0.002 PHE B 593 TYR 0.041 0.008 TYR B 507 ARG 0.022 0.003 ARG A 547 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 1.220 Fit side-chains revert: symmetry clash REVERT: A 395 LYS cc_start: 0.7739 (pttm) cc_final: 0.7079 (mttp) REVERT: A 665 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7724 (t80) REVERT: B 497 ASP cc_start: 0.7411 (t70) cc_final: 0.7027 (t0) REVERT: B 615 MET cc_start: 0.7353 (mtt) cc_final: 0.7121 (mtp) REVERT: B 694 MET cc_start: 0.6694 (mpp) cc_final: 0.5979 (mpp) outliers start: 16 outliers final: 7 residues processed: 155 average time/residue: 0.2151 time to fit residues: 48.1678 Evaluate side-chains 125 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 720 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 62 optimal weight: 0.2980 chunk 49 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 ASN A 458 ASN A 489 GLN A 651 GLN A 757 GLN B 341 HIS ** B 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN B 519 HIS B 569 ASN B 611 ASN B 651 GLN B 652 ASN ** B 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 795 HIS C 32 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.179526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.144330 restraints weight = 13072.937| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.46 r_work: 0.3691 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10461 Z= 0.200 Angle : 0.573 7.488 14131 Z= 0.302 Chirality : 0.042 0.164 1536 Planarity : 0.004 0.043 1802 Dihedral : 4.992 53.903 1354 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.24 % Allowed : 10.40 % Favored : 88.36 % 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: 1.20 (0.24), residues: 1225 helix: 1.27 (0.19), residues: 753 sheet: -0.71 (0.55), residues: 77 loop : 0.40 (0.33), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 731 HIS 0.003 0.001 HIS B 341 PHE 0.014 0.001 PHE B 593 TYR 0.020 0.002 TYR B 351 ARG 0.006 0.000 ARG A 547 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 1.171 Fit side-chains REVERT: A 355 ASN cc_start: 0.4999 (m110) cc_final: 0.4656 (p0) REVERT: A 360 ASN cc_start: 0.6936 (p0) cc_final: 0.6600 (p0) REVERT: A 363 ASN cc_start: 0.7606 (t0) cc_final: 0.7352 (t0) REVERT: A 395 LYS cc_start: 0.7884 (pttm) cc_final: 0.7177 (mttp) REVERT: A 665 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.7490 (t80) REVERT: A 750 ASP cc_start: 0.6833 (m-30) cc_final: 0.6615 (m-30) REVERT: B 237 SER cc_start: 0.7736 (m) cc_final: 0.7110 (t) REVERT: B 241 GLN cc_start: 0.6813 (OUTLIER) cc_final: 0.6187 (mp10) REVERT: B 283 ASP cc_start: 0.7845 (t70) cc_final: 0.7411 (t70) REVERT: B 497 ASP cc_start: 0.7277 (t70) cc_final: 0.6936 (t0) REVERT: B 694 MET cc_start: 0.6555 (mpp) cc_final: 0.5853 (mpp) REVERT: B 764 MET cc_start: 0.6498 (OUTLIER) cc_final: 0.6134 (mtp) outliers start: 14 outliers final: 2 residues processed: 168 average time/residue: 0.2057 time to fit residues: 50.4786 Evaluate side-chains 134 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 129 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 764 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 91 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 17 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 HIS ** B 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN B 569 ASN B 734 GLN ** B 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.178521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.143687 restraints weight = 13273.979| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.43 r_work: 0.3687 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10461 Z= 0.206 Angle : 0.547 6.506 14131 Z= 0.286 Chirality : 0.042 0.165 1536 Planarity : 0.004 0.046 1802 Dihedral : 4.571 56.203 1346 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.96 % Allowed : 11.38 % Favored : 86.67 % 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: 1.39 (0.24), residues: 1225 helix: 1.48 (0.19), residues: 754 sheet: -0.56 (0.57), residues: 77 loop : 0.33 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 746 HIS 0.005 0.001 HIS B 341 PHE 0.014 0.001 PHE B 593 TYR 0.022 0.002 TYR B 788 ARG 0.005 0.000 ARG A 547 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 1.148 Fit side-chains revert: symmetry clash REVERT: A 360 ASN cc_start: 0.6853 (p0) cc_final: 0.6568 (p0) REVERT: A 549 MET cc_start: 0.7498 (tpp) cc_final: 0.7235 (tpp) REVERT: A 665 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7581 (t80) REVERT: A 750 ASP cc_start: 0.6819 (m-30) cc_final: 0.6604 (m-30) REVERT: B 404 THR cc_start: 0.7959 (m) cc_final: 0.7575 (p) REVERT: B 497 ASP cc_start: 0.7290 (t70) cc_final: 0.6940 (t0) REVERT: B 665 PHE cc_start: 0.8307 (OUTLIER) cc_final: 0.7820 (t80) REVERT: B 694 MET cc_start: 0.6683 (mpp) cc_final: 0.5965 (mpp) REVERT: B 764 MET cc_start: 0.6415 (OUTLIER) cc_final: 0.6046 (mtp) outliers start: 22 outliers final: 10 residues processed: 157 average time/residue: 0.2078 time to fit residues: 47.4822 Evaluate side-chains 141 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 665 PHE Chi-restraints excluded: chain B residue 764 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 15 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** B 748 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 = 0.4175 r_free = 0.4175 target = 0.176063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.140695 restraints weight = 13178.655| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.46 r_work: 0.3649 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10461 Z= 0.245 Angle : 0.564 6.330 14131 Z= 0.296 Chirality : 0.043 0.166 1536 Planarity : 0.004 0.048 1802 Dihedral : 4.607 57.485 1346 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.96 % Allowed : 13.24 % Favored : 84.80 % 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: 1.36 (0.24), residues: 1225 helix: 1.52 (0.19), residues: 747 sheet: -0.51 (0.58), residues: 77 loop : 0.17 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 245 HIS 0.003 0.001 HIS B 262 PHE 0.019 0.002 PHE A 261 TYR 0.022 0.002 TYR B 788 ARG 0.004 0.000 ARG B 238 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 1.283 Fit side-chains revert: symmetry clash REVERT: A 313 ARG cc_start: 0.6697 (mtm180) cc_final: 0.6359 (mtm180) REVERT: A 360 ASN cc_start: 0.6809 (p0) cc_final: 0.6524 (p0) REVERT: A 665 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.7711 (t80) REVERT: A 750 ASP cc_start: 0.6877 (m-30) cc_final: 0.6677 (m-30) REVERT: B 404 THR cc_start: 0.8080 (m) cc_final: 0.7654 (p) REVERT: B 497 ASP cc_start: 0.7356 (t70) cc_final: 0.7007 (t0) REVERT: B 665 PHE cc_start: 0.8383 (OUTLIER) cc_final: 0.7850 (t80) REVERT: B 694 MET cc_start: 0.6793 (mpp) cc_final: 0.6119 (mpp) REVERT: B 764 MET cc_start: 0.6463 (OUTLIER) cc_final: 0.6069 (mtp) outliers start: 22 outliers final: 13 residues processed: 158 average time/residue: 0.2174 time to fit residues: 49.6925 Evaluate side-chains 141 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 665 PHE Chi-restraints excluded: chain B residue 764 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 54 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 65 optimal weight: 0.0980 chunk 81 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN A 360 ASN A 533 ASN ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 748 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 = 0.4190 r_free = 0.4190 target = 0.177510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.142254 restraints weight = 13246.000| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.48 r_work: 0.3672 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10461 Z= 0.193 Angle : 0.537 6.885 14131 Z= 0.282 Chirality : 0.042 0.167 1536 Planarity : 0.004 0.081 1802 Dihedral : 4.532 59.268 1346 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.04 % Allowed : 14.31 % Favored : 83.64 % 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: 1.48 (0.24), residues: 1225 helix: 1.66 (0.19), residues: 747 sheet: -0.46 (0.58), residues: 77 loop : 0.10 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 245 HIS 0.002 0.001 HIS A 519 PHE 0.021 0.001 PHE A 261 TYR 0.031 0.002 TYR A 420 ARG 0.006 0.000 ARG B 238 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 1.203 Fit side-chains revert: symmetry clash REVERT: A 313 ARG cc_start: 0.6686 (mtm180) cc_final: 0.6448 (mtm180) REVERT: A 355 ASN cc_start: 0.4745 (m-40) cc_final: 0.4434 (p0) REVERT: A 360 ASN cc_start: 0.6779 (OUTLIER) cc_final: 0.6511 (p0) REVERT: A 665 PHE cc_start: 0.8278 (OUTLIER) cc_final: 0.7659 (t80) REVERT: A 750 ASP cc_start: 0.6876 (m-30) cc_final: 0.6668 (m-30) REVERT: B 404 THR cc_start: 0.8036 (m) cc_final: 0.7566 (p) REVERT: B 497 ASP cc_start: 0.7352 (t70) cc_final: 0.6998 (t0) REVERT: B 556 TYR cc_start: 0.7507 (m-80) cc_final: 0.7122 (m-80) REVERT: B 665 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.7820 (t80) REVERT: B 694 MET cc_start: 0.6793 (mpp) cc_final: 0.6143 (mpp) REVERT: B 764 MET cc_start: 0.6514 (OUTLIER) cc_final: 0.6177 (mtp) outliers start: 23 outliers final: 12 residues processed: 155 average time/residue: 0.2116 time to fit residues: 47.8951 Evaluate side-chains 143 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 665 PHE Chi-restraints excluded: chain B residue 764 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 50 optimal weight: 0.5980 chunk 76 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 120 optimal weight: 10.0000 chunk 116 optimal weight: 0.6980 chunk 115 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 88 optimal weight: 0.2980 chunk 18 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 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 241 GLN ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 572 GLN ** B 748 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 = 0.4196 r_free = 0.4196 target = 0.178052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.143023 restraints weight = 13291.620| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 2.48 r_work: 0.3681 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10461 Z= 0.179 Angle : 0.530 7.118 14131 Z= 0.276 Chirality : 0.041 0.170 1536 Planarity : 0.004 0.065 1802 Dihedral : 4.481 59.980 1346 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.96 % Allowed : 14.49 % Favored : 83.56 % 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: 1.54 (0.24), residues: 1225 helix: 1.76 (0.19), residues: 741 sheet: -0.37 (0.57), residues: 75 loop : 0.05 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 245 HIS 0.002 0.000 HIS B 341 PHE 0.022 0.001 PHE A 261 TYR 0.030 0.002 TYR A 420 ARG 0.007 0.000 ARG B 238 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 1.210 Fit side-chains revert: symmetry clash REVERT: A 313 ARG cc_start: 0.6755 (mtm180) cc_final: 0.6548 (mtm180) REVERT: A 320 ILE cc_start: 0.7476 (OUTLIER) cc_final: 0.7210 (mt) REVERT: A 355 ASN cc_start: 0.4858 (m-40) cc_final: 0.4611 (p0) REVERT: A 665 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.7659 (t80) REVERT: A 694 MET cc_start: 0.5573 (mmp) cc_final: 0.5351 (mmp) REVERT: A 715 MET cc_start: 0.7659 (OUTLIER) cc_final: 0.7197 (ttp) REVERT: B 404 THR cc_start: 0.8009 (m) cc_final: 0.7550 (p) REVERT: B 497 ASP cc_start: 0.7340 (t70) cc_final: 0.6986 (t0) REVERT: B 556 TYR cc_start: 0.7471 (m-80) cc_final: 0.7036 (m-80) REVERT: B 665 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.7812 (t80) REVERT: B 694 MET cc_start: 0.6785 (mpp) cc_final: 0.6192 (mpp) REVERT: B 764 MET cc_start: 0.6540 (OUTLIER) cc_final: 0.6202 (mtp) outliers start: 22 outliers final: 13 residues processed: 157 average time/residue: 0.2064 time to fit residues: 47.6400 Evaluate side-chains 148 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 715 MET Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 665 PHE Chi-restraints excluded: chain B residue 764 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 50 optimal weight: 0.5980 chunk 87 optimal weight: 0.0570 chunk 71 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 10 optimal weight: 0.0270 chunk 6 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 114 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 748 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 = 0.4214 r_free = 0.4214 target = 0.179710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.144590 restraints weight = 13390.549| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 2.52 r_work: 0.3705 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10461 Z= 0.158 Angle : 0.522 7.491 14131 Z= 0.272 Chirality : 0.041 0.167 1536 Planarity : 0.004 0.049 1802 Dihedral : 4.371 59.033 1346 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.69 % Allowed : 15.47 % Favored : 82.84 % 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: 1.56 (0.24), residues: 1225 helix: 1.80 (0.19), residues: 746 sheet: -0.48 (0.56), residues: 75 loop : -0.01 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 245 HIS 0.002 0.000 HIS A 519 PHE 0.020 0.001 PHE A 261 TYR 0.021 0.002 TYR A 351 ARG 0.007 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 1.202 Fit side-chains revert: symmetry clash REVERT: A 320 ILE cc_start: 0.7416 (OUTLIER) cc_final: 0.7164 (mt) REVERT: A 355 ASN cc_start: 0.4869 (m-40) cc_final: 0.4640 (p0) REVERT: A 360 ASN cc_start: 0.6865 (p0) cc_final: 0.6480 (p0) REVERT: A 439 TYR cc_start: 0.8021 (t80) cc_final: 0.7763 (t80) REVERT: A 665 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.7750 (t80) REVERT: A 694 MET cc_start: 0.5725 (mmp) cc_final: 0.5490 (mmp) REVERT: A 715 MET cc_start: 0.7666 (OUTLIER) cc_final: 0.7192 (ttp) REVERT: B 320 ILE cc_start: 0.7137 (OUTLIER) cc_final: 0.6834 (mm) REVERT: B 404 THR cc_start: 0.8001 (m) cc_final: 0.7538 (p) REVERT: B 497 ASP cc_start: 0.7347 (t70) cc_final: 0.6988 (t0) REVERT: B 556 TYR cc_start: 0.7402 (m-80) cc_final: 0.7125 (m-80) REVERT: B 665 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.7757 (t80) REVERT: B 694 MET cc_start: 0.6836 (mpp) cc_final: 0.6202 (mpp) REVERT: B 764 MET cc_start: 0.6468 (OUTLIER) cc_final: 0.6214 (mtp) outliers start: 19 outliers final: 11 residues processed: 154 average time/residue: 0.2206 time to fit residues: 49.4887 Evaluate side-chains 142 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 715 MET Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 665 PHE Chi-restraints excluded: chain B residue 764 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 23 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 77 optimal weight: 0.0570 chunk 53 optimal weight: 0.7980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 748 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 = 0.4206 r_free = 0.4206 target = 0.178877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.143926 restraints weight = 13367.496| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.50 r_work: 0.3689 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10461 Z= 0.175 Angle : 0.532 7.190 14131 Z= 0.277 Chirality : 0.041 0.166 1536 Planarity : 0.004 0.050 1802 Dihedral : 4.343 58.324 1346 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.69 % Allowed : 15.82 % Favored : 82.49 % 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: 1.56 (0.24), residues: 1225 helix: 1.79 (0.19), residues: 748 sheet: -0.46 (0.56), residues: 75 loop : 0.00 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 342 HIS 0.002 0.000 HIS B 341 PHE 0.011 0.001 PHE B 568 TYR 0.020 0.002 TYR B 406 ARG 0.009 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 1.110 Fit side-chains revert: symmetry clash REVERT: A 320 ILE cc_start: 0.7419 (OUTLIER) cc_final: 0.7165 (mt) REVERT: A 355 ASN cc_start: 0.4911 (m-40) cc_final: 0.4703 (p0) REVERT: A 383 VAL cc_start: 0.3954 (OUTLIER) cc_final: 0.3713 (p) REVERT: A 439 TYR cc_start: 0.8043 (t80) cc_final: 0.7740 (t80) REVERT: A 665 PHE cc_start: 0.8358 (OUTLIER) cc_final: 0.7733 (t80) REVERT: A 715 MET cc_start: 0.7662 (OUTLIER) cc_final: 0.7185 (ttp) REVERT: B 320 ILE cc_start: 0.7076 (OUTLIER) cc_final: 0.6750 (mm) REVERT: B 404 THR cc_start: 0.8027 (m) cc_final: 0.7645 (p) REVERT: B 497 ASP cc_start: 0.7312 (t70) cc_final: 0.6954 (t0) REVERT: B 556 TYR cc_start: 0.7476 (m-80) cc_final: 0.7065 (m-80) REVERT: B 665 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.7760 (t80) REVERT: B 694 MET cc_start: 0.6889 (mpp) cc_final: 0.6263 (mpp) outliers start: 19 outliers final: 11 residues processed: 147 average time/residue: 0.2148 time to fit residues: 46.2031 Evaluate side-chains 147 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 715 MET Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 665 PHE Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 817 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 53 optimal weight: 0.4980 chunk 82 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN A 326 HIS ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 748 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 = 0.4201 r_free = 0.4201 target = 0.178550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.143989 restraints weight = 13433.963| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 2.38 r_work: 0.3700 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10461 Z= 0.201 Angle : 0.543 7.368 14131 Z= 0.283 Chirality : 0.041 0.167 1536 Planarity : 0.004 0.051 1802 Dihedral : 4.365 57.398 1346 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.60 % Allowed : 16.18 % Favored : 82.22 % 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: 1.56 (0.24), residues: 1225 helix: 1.81 (0.19), residues: 745 sheet: -0.40 (0.55), residues: 75 loop : -0.05 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 342 HIS 0.002 0.001 HIS B 262 PHE 0.012 0.001 PHE B 568 TYR 0.032 0.002 TYR A 277 ARG 0.008 0.000 ARG B 238 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 1.220 Fit side-chains revert: symmetry clash REVERT: A 320 ILE cc_start: 0.7476 (OUTLIER) cc_final: 0.7198 (mt) REVERT: A 355 ASN cc_start: 0.5022 (m-40) cc_final: 0.4776 (p0) REVERT: A 439 TYR cc_start: 0.8062 (t80) cc_final: 0.7719 (t80) REVERT: A 665 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.7681 (t80) REVERT: A 715 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.7169 (ttp) REVERT: B 361 MET cc_start: 0.5765 (ttt) cc_final: 0.5505 (ptm) REVERT: B 404 THR cc_start: 0.8082 (m) cc_final: 0.7641 (p) REVERT: B 497 ASP cc_start: 0.7315 (t70) cc_final: 0.6964 (t0) REVERT: B 556 TYR cc_start: 0.7502 (m-80) cc_final: 0.7049 (m-80) REVERT: B 665 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.7790 (t80) REVERT: B 694 MET cc_start: 0.7008 (mpp) cc_final: 0.6430 (mpp) outliers start: 18 outliers final: 13 residues processed: 158 average time/residue: 0.2214 time to fit residues: 50.3335 Evaluate side-chains 154 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 715 MET Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 665 PHE Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 817 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 21 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 119 optimal weight: 0.0010 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 748 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 = 0.4221 r_free = 0.4221 target = 0.180674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.145796 restraints weight = 13485.783| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 2.43 r_work: 0.3720 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10461 Z= 0.188 Angle : 0.548 9.265 14131 Z= 0.287 Chirality : 0.041 0.170 1536 Planarity : 0.004 0.050 1802 Dihedral : 4.342 56.294 1346 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.60 % Allowed : 16.27 % Favored : 82.13 % 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: 1.55 (0.24), residues: 1225 helix: 1.81 (0.19), residues: 745 sheet: -0.48 (0.55), residues: 75 loop : -0.06 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 245 HIS 0.002 0.000 HIS A 326 PHE 0.012 0.001 PHE B 568 TYR 0.019 0.002 TYR B 406 ARG 0.008 0.000 ARG B 238 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 320 ILE cc_start: 0.7384 (OUTLIER) cc_final: 0.7127 (mt) REVERT: A 355 ASN cc_start: 0.4978 (m-40) cc_final: 0.4745 (p0) REVERT: A 383 VAL cc_start: 0.4100 (OUTLIER) cc_final: 0.3832 (p) REVERT: A 439 TYR cc_start: 0.8035 (t80) cc_final: 0.7591 (t80) REVERT: A 665 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.7648 (t80) REVERT: A 715 MET cc_start: 0.7628 (OUTLIER) cc_final: 0.7146 (ttp) REVERT: B 361 MET cc_start: 0.5685 (ttt) cc_final: 0.5439 (ptm) REVERT: B 404 THR cc_start: 0.8031 (m) cc_final: 0.7607 (p) REVERT: B 497 ASP cc_start: 0.7325 (t70) cc_final: 0.6956 (t0) REVERT: B 556 TYR cc_start: 0.7475 (m-80) cc_final: 0.7024 (m-80) REVERT: B 665 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.7747 (t80) REVERT: B 694 MET cc_start: 0.6993 (mpp) cc_final: 0.6397 (mpp) REVERT: B 764 MET cc_start: 0.6577 (OUTLIER) cc_final: 0.6327 (mtp) outliers start: 18 outliers final: 11 residues processed: 154 average time/residue: 0.2160 time to fit residues: 48.3588 Evaluate side-chains 151 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 715 MET Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 320 ILE Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 665 PHE Chi-restraints excluded: chain B residue 764 MET Chi-restraints excluded: chain B residue 817 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 11 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 748 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 = 0.4213 r_free = 0.4213 target = 0.179771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.144441 restraints weight = 13477.847| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.48 r_work: 0.3691 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10461 Z= 0.208 Angle : 0.557 9.033 14131 Z= 0.292 Chirality : 0.041 0.168 1536 Planarity : 0.004 0.051 1802 Dihedral : 4.348 55.818 1346 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.42 % Allowed : 16.36 % Favored : 82.22 % 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: 1.54 (0.24), residues: 1225 helix: 1.82 (0.19), residues: 746 sheet: -0.54 (0.55), residues: 75 loop : -0.09 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 245 HIS 0.002 0.001 HIS A 326 PHE 0.015 0.001 PHE A 261 TYR 0.019 0.002 TYR B 406 ARG 0.008 0.000 ARG B 239 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4810.62 seconds wall clock time: 86 minutes 52.59 seconds (5212.59 seconds total)