Starting phenix.real_space_refine on Fri Oct 11 12:58:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vpp_43412/10_2024/8vpp_43412_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vpp_43412/10_2024/8vpp_43412.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vpp_43412/10_2024/8vpp_43412.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vpp_43412/10_2024/8vpp_43412.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vpp_43412/10_2024/8vpp_43412_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vpp_43412/10_2024/8vpp_43412_trim.cif" } resolution = 2.9 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= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 S 55 5.16 5 Cl 1 4.86 5 C 6418 2.51 5 N 1698 2.21 5 O 1755 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 9930 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 892, 6896 Classifications: {'peptide': 892} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 41, 'TRANS': 850} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'TPO:plan-1': 2, 'ASP:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 58 Chain: "B" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 3010 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 354} Chain breaks: 1 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 24 Unusual residues: {'KLT': 1} Classifications: {'undetermined': 1, 'water': 2} Link IDs: {None: 2} Time building chain proxies: 6.55, per 1000 atoms: 0.66 Number of scatterers: 9930 At special positions: 0 Unit cell: (156.87, 86.32, 113.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 55 16.00 P 3 15.00 O 1755 8.00 N 1698 7.00 C 6418 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 415 " - pdb=" SG CYS A 420 " distance=2.03 Simple disulfide: pdb=" SG CYS A 429 " - pdb=" SG CYS A 435 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.33 Conformation dependent library (CDL) restraints added in 1.2 seconds 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2336 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 2 sheets defined 60.5% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 66 through 71 removed outlier: 4.228A pdb=" N TYR A 70 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 90 Processing helix chain 'A' and resid 136 through 141 Processing helix chain 'A' and resid 141 through 150 Processing helix chain 'A' and resid 151 through 157 removed outlier: 3.950A pdb=" N TYR A 155 " --> pdb=" O GLY A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 166 Processing helix chain 'A' and resid 166 through 194 removed outlier: 3.699A pdb=" N ASN A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 210 Processing helix chain 'A' and resid 211 through 247 removed outlier: 3.554A pdb=" N SER A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 277 removed outlier: 3.738A pdb=" N GLY A 277 " --> pdb=" O ILE A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 304 removed outlier: 3.593A pdb=" N LEU A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 314 Processing helix chain 'A' and resid 320 through 327 Processing helix chain 'A' and resid 338 through 347 Processing helix chain 'A' and resid 348 through 351 removed outlier: 3.579A pdb=" N THR A 351 " --> pdb=" O PRO A 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 348 through 351' Processing helix chain 'A' and resid 356 through 363 removed outlier: 5.476A pdb=" N GLY A 361 " --> pdb=" O ASN A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 394 Proline residue: A 371 - end of helix Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 418 through 423 Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 444 through 450 Processing helix chain 'A' and resid 452 through 486 removed outlier: 3.513A pdb=" N ILE A 456 " --> pdb=" O PHE A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 496 removed outlier: 3.504A pdb=" N GLY A 495 " --> pdb=" O ILE A 491 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS A 496 " --> pdb=" O GLY A 492 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 491 through 496' Processing helix chain 'A' and resid 504 through 522 removed outlier: 3.948A pdb=" N ILE A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA A 522 " --> pdb=" O PHE A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 553 Processing helix chain 'A' and resid 565 through 584 removed outlier: 3.675A pdb=" N THR A 584 " --> pdb=" O MET A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 606 Processing helix chain 'A' and resid 613 through 633 Processing helix chain 'A' and resid 650 through 653 Processing helix chain 'A' and resid 654 through 666 removed outlier: 3.672A pdb=" N VAL A 658 " --> pdb=" O ARG A 654 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A 664 " --> pdb=" O PHE A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 702 removed outlier: 3.666A pdb=" N LEU A 688 " --> pdb=" O ARG A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 727 Processing helix chain 'A' and resid 749 through 766 removed outlier: 3.932A pdb=" N VAL A 753 " --> pdb=" O HIS A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 851 Proline residue: A 846 - end of helix Processing helix chain 'A' and resid 852 through 856 Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 872 through 878 Processing helix chain 'A' and resid 880 through 885 Processing helix chain 'A' and resid 895 through 899 removed outlier: 3.597A pdb=" N ILE A 898 " --> pdb=" O LEU A 895 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ASN A 899 " --> pdb=" O PRO A 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 895 through 899' Processing helix chain 'A' and resid 903 through 915 Processing helix chain 'A' and resid 925 through 933 removed outlier: 3.724A pdb=" N ARG A 933 " --> pdb=" O VAL A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 948 removed outlier: 3.542A pdb=" N ILE A 945 " --> pdb=" O SER A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 966 removed outlier: 3.597A pdb=" N ASP A 964 " --> pdb=" O GLU A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 997 Processing helix chain 'B' and resid 616 through 630 Processing helix chain 'B' and resid 636 through 640 Processing helix chain 'B' and resid 654 through 666 removed outlier: 3.841A pdb=" N VAL B 658 " --> pdb=" O ARG B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 702 Proline residue: B 686 - end of helix removed outlier: 3.915A pdb=" N ASN B 693 " --> pdb=" O GLN B 689 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY B 694 " --> pdb=" O LEU B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 727 Processing helix chain 'B' and resid 749 through 766 removed outlier: 3.596A pdb=" N VAL B 753 " --> pdb=" O HIS B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 823 Processing helix chain 'B' and resid 840 through 851 Proline residue: B 846 - end of helix Processing helix chain 'B' and resid 870 through 886 removed outlier: 3.734A pdb=" N SER B 883 " --> pdb=" O ILE B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 899 removed outlier: 4.248A pdb=" N ASN B 899 " --> pdb=" O PRO B 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 896 through 899' Processing helix chain 'B' and resid 903 through 914 removed outlier: 3.851A pdb=" N LYS B 908 " --> pdb=" O ALA B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 929 Processing helix chain 'B' and resid 930 through 934 removed outlier: 3.631A pdb=" N ARG B 934 " --> pdb=" O GLU B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 948 removed outlier: 3.539A pdb=" N LYS B 947 " --> pdb=" O GLU B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 964 Processing helix chain 'B' and resid 985 through 997 Processing sheet with id=AA1, first strand: chain 'A' and resid 707 through 712 removed outlier: 6.956A pdb=" N MET A 671 " --> pdb=" O PHE A 707 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N SER A 709 " --> pdb=" O MET A 671 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N CYS A 673 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL A 711 " --> pdb=" O CYS A 673 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N HIS A 675 " --> pdb=" O VAL A 711 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLY A 740 " --> pdb=" O LEU A 647 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE A 972 " --> pdb=" O ILE A1005 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ILE A1007 " --> pdb=" O ILE A 972 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE A 974 " --> pdb=" O ILE A1007 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU A 971 " --> pdb=" O THR A 829 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 707 through 712 removed outlier: 6.617A pdb=" N CYS B 644 " --> pdb=" O ILE B 672 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N GLY B 674 " --> pdb=" O CYS B 644 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL B 646 " --> pdb=" O GLY B 674 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N VAL B 676 " --> pdb=" O VAL B 646 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU B 737 " --> pdb=" O CYS B 771 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N MET B 773 " --> pdb=" O LEU B 737 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL B 739 " --> pdb=" O MET B 773 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N MET B 775 " --> pdb=" O VAL B 739 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE B 972 " --> pdb=" O ILE B1005 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ILE B1007 " --> pdb=" O ILE B 972 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ILE B 974 " --> pdb=" O ILE B1007 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 971 " --> pdb=" O THR B 829 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ILE B 830 " --> pdb=" O ARG B 861 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N PHE B 863 " --> pdb=" O ILE B 830 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE B 832 " --> pdb=" O PHE B 863 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU B 891 " --> pdb=" O ILE B 860 " (cutoff:3.500A) 537 hydrogen bonds defined for protein. 1542 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: 3.58 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2850 1.33 - 1.45: 1666 1.45 - 1.57: 5550 1.57 - 1.69: 12 1.69 - 1.82: 85 Bond restraints: 10163 Sorted by residual: bond pdb=" OG1 TPO A 55 " pdb=" P TPO A 55 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" OG1 TPO A 60 " pdb=" P TPO A 60 " ideal model delta sigma weight residual 1.717 1.611 0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" O3P TPO A 60 " pdb=" P TPO A 60 " ideal model delta sigma weight residual 1.528 1.611 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" O2P TPO A 55 " pdb=" P TPO A 55 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" O3P TPO A 55 " pdb=" P TPO A 55 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.69e+01 ... (remaining 10158 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 13704 2.83 - 5.66: 86 5.66 - 8.49: 10 8.49 - 11.32: 5 11.32 - 14.15: 3 Bond angle restraints: 13808 Sorted by residual: angle pdb=" CA PRO A 985 " pdb=" N PRO A 985 " pdb=" CD PRO A 985 " ideal model delta sigma weight residual 112.00 97.85 14.15 1.40e+00 5.10e-01 1.02e+02 angle pdb=" N PRO A 985 " pdb=" CD PRO A 985 " pdb=" CG PRO A 985 " ideal model delta sigma weight residual 103.20 94.17 9.03 1.50e+00 4.44e-01 3.63e+01 angle pdb=" O1 KLT A1101 " pdb=" S1 KLT A1101 " pdb=" O2 KLT A1101 " ideal model delta sigma weight residual 120.26 107.51 12.75 3.00e+00 1.11e-01 1.81e+01 angle pdb=" CB TPO A 55 " pdb=" OG1 TPO A 55 " pdb=" P TPO A 55 " ideal model delta sigma weight residual 119.31 106.80 12.51 3.00e+00 1.11e-01 1.74e+01 angle pdb=" N ILE A 491 " pdb=" CA ILE A 491 " pdb=" C ILE A 491 " ideal model delta sigma weight residual 113.20 109.83 3.37 9.60e-01 1.09e+00 1.23e+01 ... (remaining 13803 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.15: 5392 25.15 - 50.30: 528 50.30 - 75.45: 67 75.45 - 100.60: 10 100.60 - 125.75: 6 Dihedral angle restraints: 6003 sinusoidal: 2365 harmonic: 3638 Sorted by residual: dihedral pdb=" CA PRO B1002 " pdb=" C PRO B1002 " pdb=" N PRO B1003 " pdb=" CA PRO B1003 " ideal model delta harmonic sigma weight residual 180.00 144.23 35.77 0 5.00e+00 4.00e-02 5.12e+01 dihedral pdb=" CB CYS A 429 " pdb=" SG CYS A 429 " pdb=" SG CYS A 435 " pdb=" CB CYS A 435 " ideal model delta sinusoidal sigma weight residual 93.00 151.70 -58.70 1 1.00e+01 1.00e-02 4.61e+01 dihedral pdb=" CA GLY A 679 " pdb=" C GLY A 679 " pdb=" N PRO A 680 " pdb=" CA PRO A 680 " ideal model delta harmonic sigma weight residual 180.00 147.41 32.59 0 5.00e+00 4.00e-02 4.25e+01 ... (remaining 6000 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.064: 1555 1.064 - 2.128: 0 2.128 - 3.192: 0 3.192 - 4.256: 0 4.256 - 5.319: 1 Chirality restraints: 1556 Sorted by residual: chirality pdb=" C7 KLT A1101 " pdb=" C6 KLT A1101 " pdb=" C9 KLT A1101 " pdb=" N2 KLT A1101 " both_signs ideal model delta sigma weight residual False 2.70 -2.62 5.32 2.00e-01 2.50e+01 7.07e+02 chirality pdb=" CA ILE A 832 " pdb=" N ILE A 832 " pdb=" C ILE A 832 " pdb=" CB ILE A 832 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA ILE B1005 " pdb=" N ILE B1005 " pdb=" C ILE B1005 " pdb=" CB ILE B1005 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 ... (remaining 1553 not shown) Planarity restraints: 1741 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 984 " -0.073 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO A 985 " 0.176 5.00e-02 4.00e+02 pdb=" CA PRO A 985 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 985 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 488 " 0.053 5.00e-02 4.00e+02 7.99e-02 1.02e+01 pdb=" N PRO A 489 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO A 489 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 489 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 938 " -0.022 2.00e-02 2.50e+03 1.59e-02 6.29e+00 pdb=" CG TRP A 938 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP A 938 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP A 938 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 938 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 938 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 938 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 938 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 938 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 938 " 0.000 2.00e-02 2.50e+03 ... (remaining 1738 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 69 2.45 - 3.06: 7463 3.06 - 3.67: 15678 3.67 - 4.29: 22977 4.29 - 4.90: 37700 Nonbonded interactions: 83887 Sorted by model distance: nonbonded pdb=" OH TYR A 155 " pdb=" OG SER A 295 " model vdw 1.832 3.040 nonbonded pdb=" O THR A 351 " pdb=" OH TYR A 539 " model vdw 1.869 3.040 nonbonded pdb=" O SER A 880 " pdb=" OG SER A 883 " model vdw 1.971 3.040 nonbonded pdb=" O ILE A 878 " pdb=" N LEU A 882 " model vdw 2.003 3.120 nonbonded pdb=" O GLY A 740 " pdb=" OH TYR A 756 " model vdw 2.014 3.040 ... (remaining 83882 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: 4.310 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.450 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 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 0.109 10163 Z= 0.264 Angle : 0.654 14.154 13808 Z= 0.343 Chirality : 0.141 5.319 1556 Planarity : 0.006 0.102 1741 Dihedral : 19.235 125.751 3661 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 47.41 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.90 % Favored : 94.78 % Rotamer: Outliers : 4.30 % Allowed : 37.19 % Favored : 58.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.25), residues: 1245 helix: 1.49 (0.21), residues: 669 sheet: -1.72 (0.47), residues: 122 loop : -0.92 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP A 938 HIS 0.006 0.001 HIS A 90 PHE 0.013 0.001 PHE A 535 TYR 0.012 0.001 TYR B 756 ARG 0.004 0.000 ARG A 918 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 249 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8550 (ttt) REVERT: A 239 GLU cc_start: 0.7283 (tm-30) cc_final: 0.6217 (mp0) REVERT: A 344 SER cc_start: 0.8589 (OUTLIER) cc_final: 0.8181 (p) REVERT: A 365 ASP cc_start: 0.8052 (t70) cc_final: 0.7612 (p0) REVERT: A 527 ILE cc_start: 0.7707 (mm) cc_final: 0.7222 (pp) REVERT: A 550 SER cc_start: 0.9124 (t) cc_final: 0.8907 (m) REVERT: A 597 PHE cc_start: 0.6858 (t80) cc_final: 0.6583 (t80) REVERT: A 714 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7358 (pm20) REVERT: A 776 ARG cc_start: 0.6994 (ptm-80) cc_final: 0.6460 (ttp-110) REVERT: A 965 TYR cc_start: 0.7052 (m-10) cc_final: 0.6787 (m-10) REVERT: A 998 GLN cc_start: 0.7779 (pt0) cc_final: 0.7548 (pt0) REVERT: B 731 ARG cc_start: 0.8490 (mtt-85) cc_final: 0.8146 (mtt-85) REVERT: B 875 ARG cc_start: 0.7349 (tmm160) cc_final: 0.6995 (ttt-90) REVERT: B 1012 GLU cc_start: 0.7770 (tp30) cc_final: 0.7440 (mt-10) outliers start: 45 outliers final: 13 residues processed: 283 average time/residue: 1.0375 time to fit residues: 319.2207 Evaluate side-chains 175 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 159 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 441 ASN Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 714 GLU Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain B residue 818 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 32 optimal weight: 0.3980 chunk 64 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 114 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 ASN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 725 GLN A 816 GLN A 825 GLN A 906 HIS A 930 ASN A1010 ASN B 890 HIS B 899 ASN B 900 GLN B 930 ASN B 955 GLN ** B 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 ASN B1011 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10163 Z= 0.256 Angle : 0.802 22.846 13808 Z= 0.375 Chirality : 0.079 2.498 1556 Planarity : 0.005 0.060 1741 Dihedral : 10.504 146.140 1419 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.18 % Favored : 95.58 % Rotamer: Outliers : 7.46 % Allowed : 29.64 % Favored : 62.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % Twisted General : 0.08 % 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: 0.34 (0.24), residues: 1245 helix: 1.39 (0.20), residues: 675 sheet: -1.83 (0.43), residues: 129 loop : -0.88 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 938 HIS 0.007 0.001 HIS B 761 PHE 0.025 0.002 PHE B 664 TYR 0.023 0.002 TYR A 847 ARG 0.007 0.001 ARG B 980 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 171 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 SER cc_start: 0.8290 (t) cc_final: 0.7983 (m) REVERT: A 344 SER cc_start: 0.8500 (p) cc_final: 0.8133 (p) REVERT: A 345 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7643 (pt) REVERT: A 365 ASP cc_start: 0.7962 (t70) cc_final: 0.7676 (p0) REVERT: A 368 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8059 (tt) REVERT: A 383 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8578 (mp) REVERT: A 446 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8299 (tpp) REVERT: A 590 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7991 (mp) REVERT: A 597 PHE cc_start: 0.7053 (t80) cc_final: 0.6763 (t80) REVERT: A 632 GLU cc_start: 0.7104 (pp20) cc_final: 0.6546 (pp20) REVERT: A 776 ARG cc_start: 0.6932 (ptm-80) cc_final: 0.6258 (ttp-110) REVERT: A 825 GLN cc_start: 0.7110 (OUTLIER) cc_final: 0.6800 (pm20) REVERT: A 874 GLU cc_start: 0.6310 (OUTLIER) cc_final: 0.5810 (mm-30) REVERT: A 957 ARG cc_start: 0.7824 (tpt170) cc_final: 0.7476 (tpt170) REVERT: B 718 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7583 (mpt-90) REVERT: B 731 ARG cc_start: 0.8488 (mtt-85) cc_final: 0.8156 (mtt-85) REVERT: B 875 ARG cc_start: 0.7707 (tmm160) cc_final: 0.7480 (ttt-90) REVERT: B 909 ARG cc_start: 0.7369 (tmm-80) cc_final: 0.7071 (tmm-80) REVERT: B 932 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7419 (pmm) REVERT: B 1012 GLU cc_start: 0.7721 (tp30) cc_final: 0.7509 (mt-10) outliers start: 78 outliers final: 19 residues processed: 225 average time/residue: 0.8640 time to fit residues: 215.1050 Evaluate side-chains 170 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 142 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 825 GLN Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 875 ARG Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain B residue 718 ARG Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain B residue 932 MET Chi-restraints excluded: chain B residue 986 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 95 optimal weight: 0.0570 chunk 77 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 114 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 102 optimal weight: 0.0970 chunk 113 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 ASN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 285 GLN B 869 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 10163 Z= 0.207 Angle : 0.736 24.658 13808 Z= 0.340 Chirality : 0.072 2.206 1556 Planarity : 0.005 0.047 1741 Dihedral : 9.916 148.752 1398 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.37 % Favored : 96.39 % Rotamer: Outliers : 6.50 % Allowed : 28.01 % Favored : 65.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % Twisted General : 0.08 % 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: 0.48 (0.24), residues: 1245 helix: 1.49 (0.20), residues: 676 sheet: -1.57 (0.44), residues: 128 loop : -0.88 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 938 HIS 0.007 0.001 HIS A 636 PHE 0.020 0.001 PHE B 664 TYR 0.015 0.001 TYR B 756 ARG 0.006 0.001 ARG A1008 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 161 time to evaluate : 1.118 Fit side-chains revert: symmetry clash REVERT: A 336 ASP cc_start: 0.7870 (m-30) cc_final: 0.7296 (t0) REVERT: A 344 SER cc_start: 0.8532 (p) cc_final: 0.8172 (p) REVERT: A 345 ILE cc_start: 0.8231 (OUTLIER) cc_final: 0.7698 (pt) REVERT: A 365 ASP cc_start: 0.7913 (t70) cc_final: 0.7564 (p0) REVERT: A 368 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8104 (tt) REVERT: A 383 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8609 (mp) REVERT: A 590 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7909 (mp) REVERT: A 597 PHE cc_start: 0.7125 (t80) cc_final: 0.6812 (t80) REVERT: A 776 ARG cc_start: 0.6789 (ptm-80) cc_final: 0.6222 (ttp-110) REVERT: A 874 GLU cc_start: 0.6159 (OUTLIER) cc_final: 0.5694 (mm-30) REVERT: A 875 ARG cc_start: 0.5786 (OUTLIER) cc_final: 0.5392 (mtt90) REVERT: A 880 SER cc_start: 0.5717 (OUTLIER) cc_final: 0.5497 (p) REVERT: A 957 ARG cc_start: 0.7852 (tpt170) cc_final: 0.7636 (tpt170) REVERT: B 681 HIS cc_start: 0.2673 (OUTLIER) cc_final: 0.2356 (m-70) REVERT: B 718 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7588 (mpt-90) REVERT: B 731 ARG cc_start: 0.8471 (mtt-85) cc_final: 0.8139 (mtt-85) REVERT: B 776 ARG cc_start: 0.7920 (ttm-80) cc_final: 0.7679 (mtt-85) REVERT: B 859 LYS cc_start: 0.8451 (ttpp) cc_final: 0.8002 (tmmm) REVERT: B 875 ARG cc_start: 0.7767 (tmm160) cc_final: 0.7565 (ttt-90) REVERT: B 932 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7385 (pmm) outliers start: 68 outliers final: 20 residues processed: 205 average time/residue: 0.9505 time to fit residues: 213.6197 Evaluate side-chains 172 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 142 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 874 GLU Chi-restraints excluded: chain A residue 875 ARG Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 718 ARG Chi-restraints excluded: chain B residue 882 LEU Chi-restraints excluded: chain B residue 895 LEU Chi-restraints excluded: chain B residue 932 MET Chi-restraints excluded: chain B residue 986 SER Chi-restraints excluded: chain B residue 1020 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 121 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 109 optimal weight: 0.4980 chunk 32 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 ASN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10163 Z= 0.245 Angle : 0.728 24.454 13808 Z= 0.341 Chirality : 0.073 2.264 1556 Planarity : 0.005 0.045 1741 Dihedral : 9.864 148.011 1397 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.61 % Favored : 96.14 % Rotamer: Outliers : 6.21 % Allowed : 28.30 % Favored : 65.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.24), residues: 1245 helix: 1.35 (0.20), residues: 682 sheet: -1.33 (0.44), residues: 129 loop : -0.85 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 938 HIS 0.007 0.001 HIS A 636 PHE 0.023 0.002 PHE B 664 TYR 0.020 0.002 TYR A 601 ARG 0.010 0.001 ARG A1008 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 158 time to evaluate : 1.092 Fit side-chains revert: symmetry clash REVERT: A 239 GLU cc_start: 0.7186 (tm-30) cc_final: 0.6677 (pt0) REVERT: A 336 ASP cc_start: 0.7925 (m-30) cc_final: 0.7285 (t0) REVERT: A 344 SER cc_start: 0.8522 (p) cc_final: 0.8184 (p) REVERT: A 345 ILE cc_start: 0.8226 (tt) cc_final: 0.7646 (pt) REVERT: A 365 ASP cc_start: 0.7942 (t70) cc_final: 0.7557 (p0) REVERT: A 368 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8070 (tt) REVERT: A 383 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8600 (mp) REVERT: A 590 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7888 (mp) REVERT: A 597 PHE cc_start: 0.7230 (t80) cc_final: 0.6871 (t80) REVERT: A 776 ARG cc_start: 0.6849 (ptm-80) cc_final: 0.6303 (ttp-110) REVERT: A 874 GLU cc_start: 0.6157 (pm20) cc_final: 0.5593 (mm-30) REVERT: A 875 ARG cc_start: 0.5870 (OUTLIER) cc_final: 0.5421 (mtt90) REVERT: A 880 SER cc_start: 0.5828 (OUTLIER) cc_final: 0.5575 (p) REVERT: B 681 HIS cc_start: 0.2853 (OUTLIER) cc_final: 0.2538 (m-70) REVERT: B 731 ARG cc_start: 0.8533 (mtt-85) cc_final: 0.8271 (mtt-85) REVERT: B 859 LYS cc_start: 0.8591 (ttpp) cc_final: 0.8168 (tmmm) REVERT: B 867 GLN cc_start: 0.6895 (OUTLIER) cc_final: 0.6148 (tt0) REVERT: B 879 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8824 (mt) REVERT: B 932 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7364 (pmm) REVERT: B 934 ARG cc_start: 0.7905 (mtm180) cc_final: 0.7425 (ptt-90) REVERT: B 941 SER cc_start: 0.5898 (OUTLIER) cc_final: 0.5621 (p) outliers start: 65 outliers final: 26 residues processed: 203 average time/residue: 1.0115 time to fit residues: 224.4761 Evaluate side-chains 178 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 142 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 875 ARG Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain B residue 867 GLN Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 882 LEU Chi-restraints excluded: chain B residue 895 LEU Chi-restraints excluded: chain B residue 913 MET Chi-restraints excluded: chain B residue 932 MET Chi-restraints excluded: chain B residue 941 SER Chi-restraints excluded: chain B residue 986 SER Chi-restraints excluded: chain B residue 1020 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 ASN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1013 ASN B 890 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10163 Z= 0.275 Angle : 0.741 24.251 13808 Z= 0.347 Chirality : 0.074 2.336 1556 Planarity : 0.005 0.045 1741 Dihedral : 9.862 147.176 1397 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.86 % Favored : 95.90 % Rotamer: Outliers : 6.50 % Allowed : 27.72 % Favored : 65.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.24), residues: 1245 helix: 1.21 (0.20), residues: 681 sheet: -1.13 (0.44), residues: 125 loop : -0.76 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 938 HIS 0.005 0.001 HIS A 636 PHE 0.027 0.002 PHE B 664 TYR 0.018 0.002 TYR B 756 ARG 0.009 0.001 ARG A1001 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 149 time to evaluate : 1.153 Fit side-chains revert: symmetry clash REVERT: A 156 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8850 (mt) REVERT: A 239 GLU cc_start: 0.7184 (tm-30) cc_final: 0.6617 (mt-10) REVERT: A 336 ASP cc_start: 0.7938 (m-30) cc_final: 0.7268 (t0) REVERT: A 344 SER cc_start: 0.8564 (p) cc_final: 0.8229 (p) REVERT: A 345 ILE cc_start: 0.8277 (tt) cc_final: 0.7634 (pt) REVERT: A 364 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7892 (ttpt) REVERT: A 383 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8581 (mp) REVERT: A 590 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7967 (mp) REVERT: A 597 PHE cc_start: 0.7312 (t80) cc_final: 0.6974 (t80) REVERT: A 859 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.7384 (ttmm) REVERT: A 875 ARG cc_start: 0.5975 (OUTLIER) cc_final: 0.5445 (mtt90) REVERT: A 880 SER cc_start: 0.5872 (OUTLIER) cc_final: 0.5576 (p) REVERT: A 894 ILE cc_start: 0.7749 (mm) cc_final: 0.7419 (mt) REVERT: A 900 GLN cc_start: 0.7028 (pp30) cc_final: 0.6766 (pp30) REVERT: A 998 GLN cc_start: 0.7415 (pt0) cc_final: 0.7189 (pt0) REVERT: B 681 HIS cc_start: 0.3103 (OUTLIER) cc_final: 0.2721 (m-70) REVERT: B 731 ARG cc_start: 0.8589 (mtt-85) cc_final: 0.8323 (mtt-85) REVERT: B 867 GLN cc_start: 0.6890 (OUTLIER) cc_final: 0.5894 (tt0) REVERT: B 909 ARG cc_start: 0.7526 (tmm-80) cc_final: 0.7176 (tmm-80) REVERT: B 934 ARG cc_start: 0.7923 (mtm180) cc_final: 0.7571 (ptt180) outliers start: 68 outliers final: 24 residues processed: 193 average time/residue: 1.0249 time to fit residues: 215.6596 Evaluate side-chains 171 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 138 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 364 LYS Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 859 LYS Chi-restraints excluded: chain A residue 875 ARG Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 718 ARG Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain B residue 867 GLN Chi-restraints excluded: chain B residue 895 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 986 SER Chi-restraints excluded: chain B residue 1020 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.0870 chunk 109 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 121 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 ASN ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1013 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10163 Z= 0.208 Angle : 0.714 25.121 13808 Z= 0.331 Chirality : 0.070 2.173 1556 Planarity : 0.005 0.046 1741 Dihedral : 9.783 149.587 1397 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.94 % Favored : 95.82 % Rotamer: Outliers : 5.26 % Allowed : 29.45 % Favored : 65.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.24), residues: 1245 helix: 1.39 (0.20), residues: 682 sheet: -0.95 (0.43), residues: 128 loop : -0.73 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 938 HIS 0.004 0.001 HIS B 761 PHE 0.022 0.001 PHE B 664 TYR 0.020 0.001 TYR A 847 ARG 0.007 0.000 ARG B 875 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 146 time to evaluate : 1.133 Fit side-chains REVERT: A 156 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8852 (mt) REVERT: A 239 GLU cc_start: 0.7183 (tm-30) cc_final: 0.6614 (mt-10) REVERT: A 336 ASP cc_start: 0.7873 (m-30) cc_final: 0.7322 (t0) REVERT: A 344 SER cc_start: 0.8569 (p) cc_final: 0.8275 (p) REVERT: A 365 ASP cc_start: 0.7806 (t0) cc_final: 0.7587 (p0) REVERT: A 383 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8597 (mp) REVERT: A 590 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7924 (mp) REVERT: A 597 PHE cc_start: 0.7271 (t80) cc_final: 0.6985 (t80) REVERT: A 606 LYS cc_start: 0.8357 (tppt) cc_final: 0.7365 (mppt) REVERT: A 859 LYS cc_start: 0.7619 (mmtm) cc_final: 0.7361 (ttmm) REVERT: A 875 ARG cc_start: 0.6121 (OUTLIER) cc_final: 0.5460 (tpp80) REVERT: A 880 SER cc_start: 0.5956 (OUTLIER) cc_final: 0.5689 (p) REVERT: A 889 PHE cc_start: 0.6366 (m-80) cc_final: 0.5960 (m-80) REVERT: A 900 GLN cc_start: 0.7065 (pp30) cc_final: 0.6750 (pp30) REVERT: A 957 ARG cc_start: 0.7700 (tpt170) cc_final: 0.7342 (tpt170) REVERT: A 998 GLN cc_start: 0.7312 (pt0) cc_final: 0.7028 (pt0) REVERT: B 681 HIS cc_start: 0.3006 (OUTLIER) cc_final: 0.2653 (m-70) REVERT: B 731 ARG cc_start: 0.8544 (mtt-85) cc_final: 0.8281 (mtt-85) REVERT: B 867 GLN cc_start: 0.6700 (OUTLIER) cc_final: 0.5624 (tt0) REVERT: B 871 MET cc_start: 0.6801 (mtm) cc_final: 0.6596 (mmm) REVERT: B 909 ARG cc_start: 0.7435 (tmm-80) cc_final: 0.7123 (tmm-80) REVERT: B 932 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7343 (pmm) REVERT: B 934 ARG cc_start: 0.7921 (mtm180) cc_final: 0.7603 (ptt180) REVERT: B 941 SER cc_start: 0.6048 (OUTLIER) cc_final: 0.5786 (p) REVERT: B 1000 LEU cc_start: 0.5785 (OUTLIER) cc_final: 0.5531 (pp) outliers start: 55 outliers final: 23 residues processed: 189 average time/residue: 0.9884 time to fit residues: 204.7663 Evaluate side-chains 171 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 138 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 875 ARG Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain B residue 867 GLN Chi-restraints excluded: chain B residue 895 LEU Chi-restraints excluded: chain B residue 932 MET Chi-restraints excluded: chain B residue 941 SER Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 986 SER Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain B residue 1020 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.8980 chunk 69 optimal weight: 0.0050 chunk 89 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 76 optimal weight: 0.0370 chunk 74 optimal weight: 0.0000 chunk 56 optimal weight: 0.5980 chunk 75 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 overall best weight: 0.2876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 ASN ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 ASN A1013 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10163 Z= 0.172 Angle : 0.700 25.580 13808 Z= 0.324 Chirality : 0.068 2.085 1556 Planarity : 0.004 0.045 1741 Dihedral : 9.686 150.910 1397 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.02 % Favored : 95.74 % Rotamer: Outliers : 4.40 % Allowed : 30.50 % Favored : 65.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.24), residues: 1245 helix: 1.62 (0.20), residues: 678 sheet: -0.64 (0.44), residues: 127 loop : -0.56 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A 938 HIS 0.004 0.001 HIS B 761 PHE 0.018 0.001 PHE B 664 TYR 0.020 0.001 TYR A 601 ARG 0.006 0.000 ARG A1008 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 148 time to evaluate : 1.154 Fit side-chains REVERT: A 239 GLU cc_start: 0.7188 (tm-30) cc_final: 0.6665 (pt0) REVERT: A 257 ASN cc_start: 0.7592 (p0) cc_final: 0.7256 (t0) REVERT: A 336 ASP cc_start: 0.7813 (m-30) cc_final: 0.7399 (t0) REVERT: A 344 SER cc_start: 0.8530 (p) cc_final: 0.8217 (p) REVERT: A 345 ILE cc_start: 0.8182 (tt) cc_final: 0.7641 (pt) REVERT: A 364 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7941 (ttpt) REVERT: A 365 ASP cc_start: 0.7791 (t0) cc_final: 0.7561 (p0) REVERT: A 590 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7882 (mp) REVERT: A 597 PHE cc_start: 0.7206 (t80) cc_final: 0.6887 (t80) REVERT: A 606 LYS cc_start: 0.8375 (tppt) cc_final: 0.7379 (mppt) REVERT: A 880 SER cc_start: 0.6031 (OUTLIER) cc_final: 0.5829 (p) REVERT: A 960 GLU cc_start: 0.7001 (tt0) cc_final: 0.6770 (tp30) REVERT: A 967 ARG cc_start: 0.6768 (ttp-110) cc_final: 0.6515 (mtp85) REVERT: A 998 GLN cc_start: 0.7194 (pt0) cc_final: 0.6898 (pt0) REVERT: B 681 HIS cc_start: 0.3039 (OUTLIER) cc_final: 0.2680 (m-70) REVERT: B 731 ARG cc_start: 0.8485 (mtt-85) cc_final: 0.8228 (mtt-85) REVERT: B 867 GLN cc_start: 0.6570 (OUTLIER) cc_final: 0.6266 (tm-30) REVERT: B 871 MET cc_start: 0.6737 (mtm) cc_final: 0.6521 (mmm) REVERT: B 909 ARG cc_start: 0.7408 (tmm-80) cc_final: 0.7109 (tmm-80) REVERT: B 914 ILE cc_start: 0.7423 (tt) cc_final: 0.7159 (tp) REVERT: B 932 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7305 (pmm) REVERT: B 934 ARG cc_start: 0.7872 (mtm180) cc_final: 0.7487 (ptt-90) REVERT: B 941 SER cc_start: 0.5988 (OUTLIER) cc_final: 0.5700 (p) outliers start: 46 outliers final: 20 residues processed: 183 average time/residue: 0.9723 time to fit residues: 195.0131 Evaluate side-chains 163 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 136 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 364 LYS Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain A residue 1013 ASN Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 867 GLN Chi-restraints excluded: chain B residue 895 LEU Chi-restraints excluded: chain B residue 932 MET Chi-restraints excluded: chain B residue 941 SER Chi-restraints excluded: chain B residue 986 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 77 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 106 optimal weight: 0.0470 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 ASN A1013 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10163 Z= 0.207 Angle : 0.715 25.165 13808 Z= 0.332 Chirality : 0.069 2.149 1556 Planarity : 0.004 0.045 1741 Dihedral : 9.647 149.787 1397 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.86 % Favored : 95.90 % Rotamer: Outliers : 4.40 % Allowed : 30.31 % Favored : 65.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.24), residues: 1245 helix: 1.61 (0.20), residues: 682 sheet: -0.47 (0.44), residues: 126 loop : -0.60 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 938 HIS 0.004 0.001 HIS B 761 PHE 0.022 0.001 PHE B 664 TYR 0.014 0.001 TYR B 756 ARG 0.006 0.000 ARG A1008 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 142 time to evaluate : 1.221 Fit side-chains revert: symmetry clash REVERT: A 239 GLU cc_start: 0.7157 (tm-30) cc_final: 0.6626 (mt-10) REVERT: A 257 ASN cc_start: 0.7590 (p0) cc_final: 0.7276 (t0) REVERT: A 336 ASP cc_start: 0.7750 (m-30) cc_final: 0.7289 (t0) REVERT: A 344 SER cc_start: 0.8550 (p) cc_final: 0.8260 (p) REVERT: A 364 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7956 (ttpt) REVERT: A 365 ASP cc_start: 0.7817 (t0) cc_final: 0.7557 (p0) REVERT: A 383 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8617 (mp) REVERT: A 597 PHE cc_start: 0.7190 (t80) cc_final: 0.6911 (t80) REVERT: A 606 LYS cc_start: 0.8442 (tppt) cc_final: 0.7463 (mppt) REVERT: A 875 ARG cc_start: 0.6188 (OUTLIER) cc_final: 0.5231 (tpp80) REVERT: A 900 GLN cc_start: 0.7032 (pp30) cc_final: 0.6623 (pp30) REVERT: A 967 ARG cc_start: 0.6794 (ttp-110) cc_final: 0.6314 (mtp85) REVERT: A 986 SER cc_start: 0.7468 (OUTLIER) cc_final: 0.7043 (t) REVERT: A 998 GLN cc_start: 0.7230 (pt0) cc_final: 0.6954 (pt0) REVERT: B 681 HIS cc_start: 0.3110 (OUTLIER) cc_final: 0.2764 (m-70) REVERT: B 731 ARG cc_start: 0.8509 (mtt-85) cc_final: 0.8247 (mtt-85) REVERT: B 867 GLN cc_start: 0.6588 (OUTLIER) cc_final: 0.6363 (tm-30) REVERT: B 909 ARG cc_start: 0.7419 (tmm-80) cc_final: 0.7112 (tmm-80) REVERT: B 914 ILE cc_start: 0.7423 (tt) cc_final: 0.7162 (tp) REVERT: B 932 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7316 (pmm) REVERT: B 934 ARG cc_start: 0.7901 (mtm180) cc_final: 0.7538 (ptt-90) outliers start: 46 outliers final: 24 residues processed: 178 average time/residue: 1.0254 time to fit residues: 198.7978 Evaluate side-chains 166 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 135 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 364 LYS Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 875 ARG Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain B residue 867 GLN Chi-restraints excluded: chain B residue 895 LEU Chi-restraints excluded: chain B residue 932 MET Chi-restraints excluded: chain B residue 986 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.0980 chunk 116 optimal weight: 0.0060 chunk 68 optimal weight: 0.1980 chunk 49 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 119 optimal weight: 0.7980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 ASN A 432 GLN A 906 HIS A1013 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10163 Z= 0.183 Angle : 0.715 25.307 13808 Z= 0.332 Chirality : 0.068 2.103 1556 Planarity : 0.004 0.044 1741 Dihedral : 9.588 150.630 1397 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.61 % Favored : 96.14 % Rotamer: Outliers : 4.49 % Allowed : 30.69 % Favored : 64.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.24), residues: 1245 helix: 1.70 (0.20), residues: 682 sheet: -0.46 (0.44), residues: 127 loop : -0.57 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP A 938 HIS 0.004 0.001 HIS B 761 PHE 0.020 0.001 PHE B 664 TYR 0.014 0.001 TYR B 756 ARG 0.011 0.001 ARG A1001 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 143 time to evaluate : 1.137 Fit side-chains revert: symmetry clash REVERT: A 239 GLU cc_start: 0.7151 (tm-30) cc_final: 0.6653 (pt0) REVERT: A 257 ASN cc_start: 0.7533 (p0) cc_final: 0.7210 (t0) REVERT: A 336 ASP cc_start: 0.7705 (m-30) cc_final: 0.7327 (t0) REVERT: A 344 SER cc_start: 0.8553 (p) cc_final: 0.8258 (p) REVERT: A 365 ASP cc_start: 0.7794 (t0) cc_final: 0.7538 (p0) REVERT: A 383 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8638 (mp) REVERT: A 597 PHE cc_start: 0.7180 (t80) cc_final: 0.6868 (t80) REVERT: A 606 LYS cc_start: 0.8385 (tppt) cc_final: 0.7278 (mppt) REVERT: A 875 ARG cc_start: 0.6328 (OUTLIER) cc_final: 0.5452 (mtt90) REVERT: A 900 GLN cc_start: 0.6959 (pp30) cc_final: 0.6652 (pp30) REVERT: A 960 GLU cc_start: 0.7280 (tp30) cc_final: 0.6631 (tt0) REVERT: A 967 ARG cc_start: 0.6674 (ttp-110) cc_final: 0.6370 (mtp85) REVERT: A 986 SER cc_start: 0.7520 (OUTLIER) cc_final: 0.7126 (t) REVERT: A 998 GLN cc_start: 0.7194 (pt0) cc_final: 0.6908 (pt0) REVERT: B 681 HIS cc_start: 0.3103 (OUTLIER) cc_final: 0.2797 (m-70) REVERT: B 731 ARG cc_start: 0.8459 (mtt-85) cc_final: 0.8225 (mtt-85) REVERT: B 909 ARG cc_start: 0.7426 (tmm-80) cc_final: 0.7128 (tmm-80) REVERT: B 914 ILE cc_start: 0.7396 (tt) cc_final: 0.7146 (tp) REVERT: B 924 LYS cc_start: 0.5944 (mptt) cc_final: 0.5557 (mppt) REVERT: B 932 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7244 (pmm) REVERT: B 934 ARG cc_start: 0.7886 (mtm180) cc_final: 0.7494 (ptt-90) outliers start: 47 outliers final: 28 residues processed: 180 average time/residue: 1.0203 time to fit residues: 201.1125 Evaluate side-chains 168 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 135 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 875 ARG Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 664 PHE Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 718 ARG Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain B residue 895 LEU Chi-restraints excluded: chain B residue 932 MET Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 965 TYR Chi-restraints excluded: chain B residue 986 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 83 optimal weight: 0.2980 chunk 125 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1013 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10163 Z= 0.202 Angle : 0.728 25.096 13808 Z= 0.338 Chirality : 0.070 2.152 1556 Planarity : 0.005 0.048 1741 Dihedral : 9.559 149.703 1397 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.69 % Favored : 96.06 % Rotamer: Outliers : 3.35 % Allowed : 32.22 % Favored : 64.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.24), residues: 1245 helix: 1.71 (0.20), residues: 682 sheet: -0.52 (0.44), residues: 130 loop : -0.62 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP A 938 HIS 0.003 0.001 HIS B 761 PHE 0.021 0.001 PHE B 664 TYR 0.019 0.001 TYR A 601 ARG 0.010 0.001 ARG A1001 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 137 time to evaluate : 1.265 Fit side-chains revert: symmetry clash REVERT: A 239 GLU cc_start: 0.7184 (tm-30) cc_final: 0.6634 (mt-10) REVERT: A 257 ASN cc_start: 0.7607 (p0) cc_final: 0.7306 (t0) REVERT: A 336 ASP cc_start: 0.7743 (m-30) cc_final: 0.7275 (t0) REVERT: A 344 SER cc_start: 0.8576 (p) cc_final: 0.8286 (p) REVERT: A 365 ASP cc_start: 0.7729 (t0) cc_final: 0.7458 (p0) REVERT: A 383 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8598 (mp) REVERT: A 590 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7867 (mp) REVERT: A 597 PHE cc_start: 0.7159 (t80) cc_final: 0.6873 (t80) REVERT: A 606 LYS cc_start: 0.8376 (tppt) cc_final: 0.7271 (mppt) REVERT: A 900 GLN cc_start: 0.6935 (pp30) cc_final: 0.5964 (pp30) REVERT: A 957 ARG cc_start: 0.7350 (tpt170) cc_final: 0.6798 (tpm-80) REVERT: A 960 GLU cc_start: 0.7488 (tp30) cc_final: 0.6666 (tt0) REVERT: A 967 ARG cc_start: 0.6640 (ttp-110) cc_final: 0.6344 (mtp85) REVERT: A 986 SER cc_start: 0.7568 (OUTLIER) cc_final: 0.7172 (t) REVERT: A 998 GLN cc_start: 0.7247 (pt0) cc_final: 0.6922 (pt0) REVERT: B 731 ARG cc_start: 0.8492 (mtt-85) cc_final: 0.8241 (mtt-85) REVERT: B 909 ARG cc_start: 0.7425 (tmm-80) cc_final: 0.7117 (tmm-80) REVERT: B 914 ILE cc_start: 0.7424 (tt) cc_final: 0.7167 (tp) REVERT: B 924 LYS cc_start: 0.5967 (mptt) cc_final: 0.5603 (mppt) REVERT: B 932 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7242 (pmm) REVERT: B 934 ARG cc_start: 0.7886 (mtm180) cc_final: 0.7513 (ptt-90) outliers start: 35 outliers final: 26 residues processed: 164 average time/residue: 0.9905 time to fit residues: 178.1757 Evaluate side-chains 165 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 135 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 875 ARG Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1013 ASN Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 664 PHE Chi-restraints excluded: chain B residue 718 ARG Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain B residue 895 LEU Chi-restraints excluded: chain B residue 932 MET Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 965 TYR Chi-restraints excluded: chain B residue 986 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.155447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.121392 restraints weight = 13239.526| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.20 r_work: 0.3301 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.144 10163 Z= 0.290 Angle : 0.985 59.147 13808 Z= 0.534 Chirality : 0.072 2.152 1556 Planarity : 0.004 0.045 1741 Dihedral : 9.570 149.702 1397 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.78 % Favored : 95.98 % Rotamer: Outliers : 3.25 % Allowed : 32.03 % Favored : 64.72 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.24), residues: 1245 helix: 1.70 (0.20), residues: 682 sheet: -0.52 (0.43), residues: 130 loop : -0.63 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 938 HIS 0.003 0.001 HIS B 761 PHE 0.021 0.001 PHE B 664 TYR 0.014 0.001 TYR B 756 ARG 0.006 0.000 ARG B 875 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4202.11 seconds wall clock time: 76 minutes 4.92 seconds (4564.92 seconds total)