Starting phenix.real_space_refine on Thu Jan 16 21:01:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vpp_43412/01_2025/8vpp_43412_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vpp_43412/01_2025/8vpp_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/cci-nas-00/data/ceres_data/8vpp_43412/01_2025/8vpp_43412.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vpp_43412/01_2025/8vpp_43412.map" model { file = "/net/cci-nas-00/data/ceres_data/8vpp_43412/01_2025/8vpp_43412_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vpp_43412/01_2025/8vpp_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 7.23, per 1000 atoms: 0.73 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: 2.70 Conformation dependent library (CDL) restraints added in 1.1 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: 2.87 Time building geometry restraints manager: 3.04 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: 4.680 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: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.500 Find NCS groups from input model: 0.110 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: 0.000 Load rotamer database and sin/cos tables:13.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.050 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 45 poor density : 249 time to evaluate : 1.040 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: 1.0444 time to fit residues: 321.0113 Evaluate side-chains 175 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.155623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.121254 restraints weight = 13190.821| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.22 r_work: 0.3304 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 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 to be fit. rotamer outliers: 78 poor density : 171 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 SER cc_start: 0.8378 (t) cc_final: 0.8146 (m) REVERT: A 344 SER cc_start: 0.8777 (p) cc_final: 0.8456 (p) REVERT: A 345 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.7945 (pt) REVERT: A 368 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8312 (tt) REVERT: A 383 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8769 (mp) REVERT: A 446 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8540 (tpp) REVERT: A 590 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8293 (mp) REVERT: A 597 PHE cc_start: 0.7480 (t80) cc_final: 0.7206 (t80) REVERT: A 632 GLU cc_start: 0.7135 (pp20) cc_final: 0.6621 (pp20) REVERT: A 776 ARG cc_start: 0.7151 (ptm-80) cc_final: 0.6536 (ttp-110) REVERT: A 825 GLN cc_start: 0.7026 (OUTLIER) cc_final: 0.6799 (pm20) REVERT: A 874 GLU cc_start: 0.6118 (OUTLIER) cc_final: 0.5724 (mm-30) REVERT: A 957 ARG cc_start: 0.7891 (tpt170) cc_final: 0.7559 (tpt170) REVERT: B 731 ARG cc_start: 0.8665 (mtt-85) cc_final: 0.8374 (mtt-85) REVERT: B 909 ARG cc_start: 0.7541 (tmm-80) cc_final: 0.7241 (tmm-80) REVERT: B 932 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7371 (pmm) outliers start: 78 outliers final: 19 residues processed: 225 average time/residue: 0.8638 time to fit residues: 215.3152 Evaluate side-chains 169 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 142 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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 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 64 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 69 optimal weight: 0.0470 chunk 30 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 25 optimal weight: 0.0670 chunk 14 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.154074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.119050 restraints weight = 13488.371| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.33 r_work: 0.3283 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10163 Z= 0.214 Angle : 0.741 24.689 13808 Z= 0.342 Chirality : 0.072 2.209 1556 Planarity : 0.005 0.047 1741 Dihedral : 9.923 148.732 1398 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.45 % Favored : 96.31 % Rotamer: Outliers : 6.60 % Allowed : 28.20 % Favored : 65.20 % 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: 0.47 (0.24), residues: 1245 helix: 1.48 (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 0.028 0.001 TRP A 938 HIS 0.005 0.001 HIS B 761 PHE 0.020 0.001 PHE B 664 TYR 0.015 0.001 TYR B 756 ARG 0.007 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 232 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 163 time to evaluate : 1.078 Fit side-chains revert: symmetry clash REVERT: A 293 MET cc_start: 0.8989 (mmm) cc_final: 0.8721 (mmp) REVERT: A 336 ASP cc_start: 0.7885 (m-30) cc_final: 0.7392 (t0) REVERT: A 344 SER cc_start: 0.8790 (p) cc_final: 0.8447 (p) REVERT: A 345 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.7936 (pt) REVERT: A 383 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8738 (mp) REVERT: A 446 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8512 (ttt) REVERT: A 590 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8179 (mp) REVERT: A 597 PHE cc_start: 0.7467 (t80) cc_final: 0.7172 (t80) REVERT: A 621 ASN cc_start: 0.8935 (m110) cc_final: 0.8724 (m110) REVERT: A 776 ARG cc_start: 0.6996 (ptm-80) cc_final: 0.6436 (ttp-110) REVERT: A 874 GLU cc_start: 0.6037 (OUTLIER) cc_final: 0.5627 (mm-30) REVERT: A 875 ARG cc_start: 0.5817 (OUTLIER) cc_final: 0.5463 (mtt90) REVERT: A 880 SER cc_start: 0.5634 (OUTLIER) cc_final: 0.5430 (p) REVERT: A 944 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7813 (mp0) REVERT: A 957 ARG cc_start: 0.7900 (tpt170) cc_final: 0.7689 (tpt170) REVERT: B 681 HIS cc_start: 0.2809 (OUTLIER) cc_final: 0.2438 (m-70) REVERT: B 731 ARG cc_start: 0.8642 (mtt-85) cc_final: 0.8409 (mtt-85) REVERT: B 776 ARG cc_start: 0.7909 (ttm-80) cc_final: 0.7664 (mtt-85) REVERT: B 859 LYS cc_start: 0.8572 (ttpp) cc_final: 0.8251 (tmmm) REVERT: B 932 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7321 (pmm) outliers start: 69 outliers final: 18 residues processed: 208 average time/residue: 0.9396 time to fit residues: 214.3628 Evaluate side-chains 173 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 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 383 ILE Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 446 MET 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 944 GLU 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 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 14 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 80 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 77 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.149525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.114296 restraints weight = 13513.328| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.31 r_work: 0.3220 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 10163 Z= 0.299 Angle : 0.750 23.910 13808 Z= 0.355 Chirality : 0.076 2.375 1556 Planarity : 0.005 0.049 1741 Dihedral : 9.924 146.407 1397 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.94 % Favored : 95.82 % Rotamer: Outliers : 6.60 % Allowed : 27.72 % Favored : 65.68 % 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: 0.27 (0.24), residues: 1245 helix: 1.19 (0.20), residues: 684 sheet: -1.39 (0.43), residues: 129 loop : -0.86 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 938 HIS 0.006 0.001 HIS A 636 PHE 0.024 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 219 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 150 time to evaluate : 1.084 Fit side-chains revert: symmetry clash REVERT: A 92 PHE cc_start: 0.6952 (OUTLIER) cc_final: 0.6648 (p90) REVERT: A 239 GLU cc_start: 0.7668 (tm-30) cc_final: 0.6979 (mt-10) REVERT: A 336 ASP cc_start: 0.7957 (m-30) cc_final: 0.7433 (t0) REVERT: A 344 SER cc_start: 0.8755 (p) cc_final: 0.8440 (p) REVERT: A 345 ILE cc_start: 0.8406 (tt) cc_final: 0.7891 (pt) REVERT: A 383 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8680 (mp) REVERT: A 446 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8483 (ttt) REVERT: A 597 PHE cc_start: 0.7543 (t80) cc_final: 0.7222 (t80) REVERT: A 621 ASN cc_start: 0.8969 (m110) cc_final: 0.8725 (m110) REVERT: A 632 GLU cc_start: 0.7446 (tm-30) cc_final: 0.7208 (tm-30) REVERT: A 859 LYS cc_start: 0.7778 (OUTLIER) cc_final: 0.7448 (ttmm) REVERT: A 874 GLU cc_start: 0.5879 (pm20) cc_final: 0.5434 (mm-30) REVERT: A 875 ARG cc_start: 0.5907 (OUTLIER) cc_final: 0.5446 (mtt90) REVERT: A 880 SER cc_start: 0.5727 (OUTLIER) cc_final: 0.5476 (p) REVERT: A 944 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7732 (mp0) REVERT: B 681 HIS cc_start: 0.2982 (OUTLIER) cc_final: 0.2583 (m-70) REVERT: B 731 ARG cc_start: 0.8712 (mtt-85) cc_final: 0.8428 (mtt-85) REVERT: B 859 LYS cc_start: 0.8618 (ttpp) cc_final: 0.8261 (tmmm) REVERT: B 867 GLN cc_start: 0.7095 (OUTLIER) cc_final: 0.6165 (tt0) REVERT: B 871 MET cc_start: 0.6896 (OUTLIER) cc_final: 0.6547 (mmm) REVERT: B 879 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8935 (mt) REVERT: B 909 ARG cc_start: 0.7577 (tmm-80) cc_final: 0.7147 (tmm-80) REVERT: B 932 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7337 (pmm) REVERT: B 934 ARG cc_start: 0.8116 (mtm180) cc_final: 0.7744 (ptt-90) outliers start: 69 outliers final: 27 residues processed: 197 average time/residue: 1.0189 time to fit residues: 218.7443 Evaluate side-chains 172 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 133 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 92 PHE 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 383 ILE Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 538 SER 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 880 SER Chi-restraints excluded: chain A residue 944 GLU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 975 THR 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 744 ASN Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain B residue 867 GLN Chi-restraints excluded: chain B residue 871 MET Chi-restraints excluded: chain B residue 879 ILE 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 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 6 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 16 optimal weight: 0.1980 chunk 44 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.150500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.115217 restraints weight = 13463.085| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.32 r_work: 0.3229 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10163 Z= 0.246 Angle : 0.729 24.387 13808 Z= 0.339 Chirality : 0.072 2.270 1556 Planarity : 0.005 0.045 1741 Dihedral : 9.849 147.930 1397 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.53 % Favored : 96.22 % Rotamer: Outliers : 6.21 % Allowed : 28.20 % Favored : 65.58 % 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: 1.26 (0.20), residues: 680 sheet: -1.16 (0.44), residues: 125 loop : -0.82 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 938 HIS 0.005 0.001 HIS A 636 PHE 0.022 0.001 PHE B 664 TYR 0.015 0.002 TYR B 756 ARG 0.008 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 208 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 143 time to evaluate : 1.657 Fit side-chains revert: symmetry clash REVERT: A 154 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8689 (tp) REVERT: A 156 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8894 (mt) REVERT: A 239 GLU cc_start: 0.7658 (tm-30) cc_final: 0.6965 (mt-10) REVERT: A 336 ASP cc_start: 0.7970 (m-30) cc_final: 0.7409 (t0) REVERT: A 344 SER cc_start: 0.8792 (p) cc_final: 0.8481 (p) REVERT: A 345 ILE cc_start: 0.8418 (tt) cc_final: 0.7846 (pt) REVERT: A 383 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8689 (mp) REVERT: A 597 PHE cc_start: 0.7609 (t80) cc_final: 0.7283 (t80) REVERT: A 621 ASN cc_start: 0.8975 (m110) cc_final: 0.8729 (m110) REVERT: A 875 ARG cc_start: 0.6009 (OUTLIER) cc_final: 0.5492 (mtt90) REVERT: A 880 SER cc_start: 0.5778 (OUTLIER) cc_final: 0.5485 (p) REVERT: A 894 ILE cc_start: 0.7775 (mm) cc_final: 0.7454 (mt) REVERT: A 900 GLN cc_start: 0.6844 (pp30) cc_final: 0.6282 (pp30) REVERT: B 681 HIS cc_start: 0.3171 (OUTLIER) cc_final: 0.2783 (m-70) REVERT: B 731 ARG cc_start: 0.8712 (mtt-85) cc_final: 0.8443 (mtt-85) REVERT: B 859 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8367 (tmmm) REVERT: B 867 GLN cc_start: 0.6994 (OUTLIER) cc_final: 0.5919 (tt0) REVERT: B 871 MET cc_start: 0.6873 (mmm) cc_final: 0.6516 (mmm) REVERT: B 909 ARG cc_start: 0.7564 (tmm-80) cc_final: 0.7204 (tmm-80) REVERT: B 934 ARG cc_start: 0.8130 (mtm180) cc_final: 0.7745 (ptt-90) outliers start: 65 outliers final: 26 residues processed: 193 average time/residue: 1.0064 time to fit residues: 214.8019 Evaluate side-chains 172 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 1.078 ------------------------------------------------------------------------------- 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 154 LEU 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 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 536 LEU Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 845 ILE 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 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 859 LYS 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 120 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 108 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 77 optimal weight: 0.0870 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.151376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.116316 restraints weight = 13464.279| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.31 r_work: 0.3247 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3802 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= 0.220 Angle : 0.719 25.091 13808 Z= 0.334 Chirality : 0.071 2.191 1556 Planarity : 0.005 0.045 1741 Dihedral : 9.767 149.297 1397 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.86 % Favored : 95.90 % Rotamer: Outliers : 5.83 % Allowed : 28.87 % 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: 0.51 (0.24), residues: 1245 helix: 1.36 (0.20), residues: 682 sheet: -1.02 (0.43), residues: 128 loop : -0.81 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 938 HIS 0.004 0.001 HIS A 636 PHE 0.023 0.001 PHE B 664 TYR 0.020 0.001 TYR A 601 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 208 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 147 time to evaluate : 1.076 Fit side-chains REVERT: A 52 CYS cc_start: 0.6903 (t) cc_final: 0.6227 (m) REVERT: A 156 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8884 (mt) REVERT: A 239 GLU cc_start: 0.7670 (tm-30) cc_final: 0.6983 (mt-10) REVERT: A 336 ASP cc_start: 0.7955 (m-30) cc_final: 0.7380 (t0) REVERT: A 344 SER cc_start: 0.8810 (p) cc_final: 0.8523 (p) REVERT: A 383 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8694 (mp) REVERT: A 597 PHE cc_start: 0.7607 (t80) cc_final: 0.7314 (t80) REVERT: A 606 LYS cc_start: 0.8883 (tppp) cc_final: 0.8644 (tppt) REVERT: A 621 ASN cc_start: 0.8976 (m110) cc_final: 0.8713 (m110) REVERT: A 848 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8228 (mt) REVERT: A 859 LYS cc_start: 0.7726 (mmtm) cc_final: 0.7520 (ttmm) REVERT: A 875 ARG cc_start: 0.6054 (OUTLIER) cc_final: 0.5420 (tpp80) REVERT: A 880 SER cc_start: 0.5840 (OUTLIER) cc_final: 0.5601 (p) REVERT: A 889 PHE cc_start: 0.6362 (m-80) cc_final: 0.6055 (m-80) REVERT: A 900 GLN cc_start: 0.6913 (pp30) cc_final: 0.6656 (pp30) REVERT: B 681 HIS cc_start: 0.3118 (OUTLIER) cc_final: 0.2707 (m-70) REVERT: B 731 ARG cc_start: 0.8686 (mtt-85) cc_final: 0.8413 (mtt-85) REVERT: B 867 GLN cc_start: 0.6920 (OUTLIER) cc_final: 0.5796 (tt0) REVERT: B 871 MET cc_start: 0.6886 (OUTLIER) cc_final: 0.6521 (mmm) REVERT: B 909 ARG cc_start: 0.7510 (tmm-80) cc_final: 0.7162 (tmm-80) REVERT: B 932 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7250 (pmm) REVERT: B 934 ARG cc_start: 0.8146 (mtm180) cc_final: 0.7774 (ptt180) outliers start: 61 outliers final: 30 residues processed: 194 average time/residue: 1.0084 time to fit residues: 213.7810 Evaluate side-chains 180 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 141 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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 388 ILE Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 486 GLN Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 848 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 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 718 ARG Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain B residue 824 GLU Chi-restraints excluded: chain B residue 867 GLN Chi-restraints excluded: chain B residue 871 MET 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 986 SER 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 64 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 47 optimal weight: 0.0020 chunk 20 optimal weight: 0.9990 chunk 2 optimal weight: 0.0870 overall best weight: 0.4566 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.153886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.118983 restraints weight = 13584.046| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.29 r_work: 0.3286 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3958 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= 0.194 Angle : 0.710 25.256 13808 Z= 0.329 Chirality : 0.069 2.133 1556 Planarity : 0.004 0.045 1741 Dihedral : 9.710 150.071 1397 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.86 % Favored : 95.90 % Rotamer: Outliers : 4.68 % Allowed : 30.11 % Favored : 65.20 % 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: 0.72 (0.24), residues: 1245 helix: 1.52 (0.20), residues: 683 sheet: -0.72 (0.43), residues: 126 loop : -0.76 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 938 HIS 0.006 0.001 HIS A 436 PHE 0.022 0.001 PHE B 664 TYR 0.014 0.001 TYR B 756 ARG 0.007 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 202 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 153 time to evaluate : 1.127 Fit side-chains REVERT: A 156 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8953 (mt) REVERT: A 239 GLU cc_start: 0.7699 (tm-30) cc_final: 0.7050 (mt-10) REVERT: A 336 ASP cc_start: 0.7910 (m-30) cc_final: 0.7513 (t0) REVERT: A 344 SER cc_start: 0.8830 (p) cc_final: 0.8543 (p) REVERT: A 345 ILE cc_start: 0.8384 (tt) cc_final: 0.7906 (pt) REVERT: A 383 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8732 (mp) REVERT: A 597 PHE cc_start: 0.7592 (t80) cc_final: 0.7308 (t80) REVERT: A 621 ASN cc_start: 0.8974 (m110) cc_final: 0.8732 (m110) REVERT: A 875 ARG cc_start: 0.6172 (OUTLIER) cc_final: 0.5515 (tpp80) REVERT: A 960 GLU cc_start: 0.7105 (tt0) cc_final: 0.6830 (tp30) REVERT: B 681 HIS cc_start: 0.3239 (OUTLIER) cc_final: 0.2779 (m-70) REVERT: B 718 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7693 (mtt-85) REVERT: B 731 ARG cc_start: 0.8642 (mtt-85) cc_final: 0.8393 (mtt-85) REVERT: B 867 GLN cc_start: 0.6899 (OUTLIER) cc_final: 0.6691 (tm-30) REVERT: B 909 ARG cc_start: 0.7551 (tmm-80) cc_final: 0.7208 (tmm-80) REVERT: B 914 ILE cc_start: 0.7627 (tt) cc_final: 0.7356 (tp) REVERT: B 932 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7269 (pmm) REVERT: B 934 ARG cc_start: 0.8134 (mtm180) cc_final: 0.7806 (ptt180) REVERT: B 941 SER cc_start: 0.6422 (OUTLIER) cc_final: 0.6156 (p) outliers start: 49 outliers final: 24 residues processed: 189 average time/residue: 1.0167 time to fit residues: 209.3222 Evaluate side-chains 169 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 1.128 ------------------------------------------------------------------------------- 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 486 GLN Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 739 VAL 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 1013 ASN 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 718 ARG Chi-restraints excluded: chain B residue 824 GLU 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 1020 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 18 optimal weight: 0.7980 chunk 72 optimal weight: 0.0170 chunk 44 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.153174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.118247 restraints weight = 13489.646| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.29 r_work: 0.3276 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10163 Z= 0.208 Angle : 0.726 25.117 13808 Z= 0.337 Chirality : 0.069 2.149 1556 Planarity : 0.005 0.047 1741 Dihedral : 9.587 149.765 1395 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.94 % Favored : 95.82 % Rotamer: Outliers : 4.40 % Allowed : 31.07 % Favored : 64.53 % 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: 0.80 (0.24), residues: 1245 helix: 1.58 (0.20), residues: 682 sheet: -0.64 (0.44), residues: 127 loop : -0.74 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 938 HIS 0.005 0.001 HIS A 636 PHE 0.023 0.001 PHE B 664 TYR 0.014 0.001 TYR B 756 ARG 0.009 0.000 ARG A1001 *********************** 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 184 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 138 time to evaluate : 1.059 Fit side-chains REVERT: A 52 CYS cc_start: 0.6915 (t) cc_final: 0.6241 (m) REVERT: A 156 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8932 (mt) REVERT: A 239 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7036 (mt-10) REVERT: A 257 ASN cc_start: 0.7860 (p0) cc_final: 0.7489 (t0) REVERT: A 336 ASP cc_start: 0.7802 (m-30) cc_final: 0.7488 (t0) REVERT: A 344 SER cc_start: 0.8825 (p) cc_final: 0.8552 (p) REVERT: A 383 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8743 (mp) REVERT: A 590 ILE cc_start: 0.8247 (mp) cc_final: 0.7887 (mp) REVERT: A 597 PHE cc_start: 0.7538 (t80) cc_final: 0.7247 (t80) REVERT: A 606 LYS cc_start: 0.8659 (tppt) cc_final: 0.7571 (mppt) REVERT: A 621 ASN cc_start: 0.8971 (m110) cc_final: 0.8714 (m110) REVERT: A 848 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8240 (mt) REVERT: A 900 GLN cc_start: 0.6764 (pp30) cc_final: 0.6350 (pp30) REVERT: B 681 HIS cc_start: 0.3172 (OUTLIER) cc_final: 0.2777 (m-70) REVERT: B 718 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7722 (mtt-85) REVERT: B 731 ARG cc_start: 0.8625 (mtt-85) cc_final: 0.8347 (mtt-85) REVERT: B 867 GLN cc_start: 0.6824 (OUTLIER) cc_final: 0.6568 (tm-30) REVERT: B 909 ARG cc_start: 0.7527 (tmm-80) cc_final: 0.7189 (tmm-80) REVERT: B 914 ILE cc_start: 0.7631 (tt) cc_final: 0.7366 (tp) REVERT: B 932 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7293 (pmm) REVERT: B 934 ARG cc_start: 0.8133 (mtm180) cc_final: 0.7754 (ptt-90) outliers start: 46 outliers final: 25 residues processed: 174 average time/residue: 1.0285 time to fit residues: 195.9793 Evaluate side-chains 163 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 1.103 ------------------------------------------------------------------------------- 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 536 LEU Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 978 ILE 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 718 ARG Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain B residue 824 GLU Chi-restraints excluded: chain B residue 867 GLN 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 963 LEU Chi-restraints excluded: chain B residue 965 TYR Chi-restraints excluded: chain B residue 986 SER Chi-restraints excluded: chain B residue 1020 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 15 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 906 HIS A1013 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.153148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.119860 restraints weight = 13358.271| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.13 r_work: 0.3273 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10163 Z= 0.238 Angle : 0.737 24.856 13808 Z= 0.347 Chirality : 0.072 2.214 1556 Planarity : 0.005 0.045 1741 Dihedral : 9.606 148.850 1395 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.10 % Favored : 95.66 % Rotamer: Outliers : 4.21 % Allowed : 31.17 % Favored : 64.63 % 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: 0.71 (0.24), residues: 1245 helix: 1.51 (0.20), residues: 682 sheet: -0.67 (0.43), residues: 129 loop : -0.79 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 938 HIS 0.004 0.001 HIS A 636 PHE 0.025 0.001 PHE B 664 TYR 0.020 0.002 TYR A 601 ARG 0.008 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 181 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 137 time to evaluate : 1.080 Fit side-chains REVERT: A 239 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7119 (mt-10) REVERT: A 257 ASN cc_start: 0.7893 (p0) cc_final: 0.7511 (t0) REVERT: A 336 ASP cc_start: 0.7808 (m-30) cc_final: 0.7417 (t0) REVERT: A 344 SER cc_start: 0.8854 (p) cc_final: 0.8596 (p) REVERT: A 383 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8729 (mp) REVERT: A 597 PHE cc_start: 0.7622 (t80) cc_final: 0.7332 (t80) REVERT: A 606 LYS cc_start: 0.8658 (tppt) cc_final: 0.7581 (mppt) REVERT: A 621 ASN cc_start: 0.8980 (m110) cc_final: 0.8727 (m110) REVERT: A 848 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8304 (mt) REVERT: A 875 ARG cc_start: 0.6434 (OUTLIER) cc_final: 0.5520 (mtt90) REVERT: A 900 GLN cc_start: 0.6830 (pp30) cc_final: 0.6016 (pp30) REVERT: A 957 ARG cc_start: 0.7443 (tpt170) cc_final: 0.6958 (tpm-80) REVERT: A 960 GLU cc_start: 0.7464 (tp30) cc_final: 0.6783 (tt0) REVERT: A 967 ARG cc_start: 0.7127 (mtp85) cc_final: 0.6801 (ttp-110) REVERT: B 681 HIS cc_start: 0.3290 (OUTLIER) cc_final: 0.3020 (m-70) REVERT: B 718 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7726 (mtt-85) REVERT: B 731 ARG cc_start: 0.8587 (mtt-85) cc_final: 0.8339 (mtt-85) REVERT: B 867 GLN cc_start: 0.6844 (OUTLIER) cc_final: 0.6643 (tm-30) REVERT: B 871 MET cc_start: 0.6933 (mmm) cc_final: 0.6550 (mmm) REVERT: B 909 ARG cc_start: 0.7588 (tmm-80) cc_final: 0.7236 (tmm-80) REVERT: B 914 ILE cc_start: 0.7706 (tt) cc_final: 0.7445 (tp) REVERT: B 924 LYS cc_start: 0.5805 (mptt) cc_final: 0.5375 (mppt) REVERT: B 932 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7176 (pmm) REVERT: B 934 ARG cc_start: 0.8151 (mtm180) cc_final: 0.7731 (ptt-90) outliers start: 44 outliers final: 28 residues processed: 173 average time/residue: 1.1017 time to fit residues: 208.2844 Evaluate side-chains 168 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL 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 739 VAL Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 848 LEU 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 1013 ASN 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 718 ARG Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain B residue 824 GLU 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 963 LEU Chi-restraints excluded: chain B residue 965 TYR Chi-restraints excluded: chain B residue 986 SER Chi-restraints excluded: chain B residue 1020 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 82 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 108 optimal weight: 0.3980 chunk 39 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 79 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 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 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 ASN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1013 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.153326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.119057 restraints weight = 13416.817| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.21 r_work: 0.3254 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10163 Z= 0.236 Angle : 0.745 24.846 13808 Z= 0.349 Chirality : 0.071 2.205 1556 Planarity : 0.005 0.045 1741 Dihedral : 9.609 148.960 1395 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.86 % Favored : 95.90 % Rotamer: Outliers : 3.44 % Allowed : 31.84 % Favored : 64.72 % 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: 0.73 (0.24), residues: 1245 helix: 1.53 (0.20), residues: 682 sheet: -0.67 (0.43), residues: 129 loop : -0.78 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP A 938 HIS 0.004 0.001 HIS B 761 PHE 0.026 0.001 PHE B 664 TYR 0.019 0.002 TYR A 847 ARG 0.007 0.001 ARG B 875 ********************** 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 to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 1.256 Fit side-chains REVERT: A 52 CYS cc_start: 0.6634 (t) cc_final: 0.5973 (m) REVERT: A 239 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7148 (mt-10) REVERT: A 257 ASN cc_start: 0.7897 (p0) cc_final: 0.7547 (t0) REVERT: A 336 ASP cc_start: 0.7784 (m-30) cc_final: 0.7411 (t0) REVERT: A 344 SER cc_start: 0.8849 (p) cc_final: 0.8588 (p) REVERT: A 383 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8774 (mp) REVERT: A 590 ILE cc_start: 0.8314 (mp) cc_final: 0.8004 (mp) REVERT: A 597 PHE cc_start: 0.7615 (t80) cc_final: 0.7310 (t80) REVERT: A 606 LYS cc_start: 0.8645 (tppt) cc_final: 0.7563 (mppt) REVERT: A 621 ASN cc_start: 0.8994 (m110) cc_final: 0.8742 (m110) REVERT: A 848 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8288 (mt) REVERT: A 900 GLN cc_start: 0.6908 (pp30) cc_final: 0.6075 (pp30) REVERT: A 957 ARG cc_start: 0.7499 (tpt170) cc_final: 0.6881 (tpm-80) REVERT: B 681 HIS cc_start: 0.3366 (OUTLIER) cc_final: 0.3143 (m-70) REVERT: B 718 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7723 (mtt-85) REVERT: B 731 ARG cc_start: 0.8592 (mtt-85) cc_final: 0.8354 (mtt-85) REVERT: B 871 MET cc_start: 0.6948 (mmm) cc_final: 0.6705 (mmm) REVERT: B 909 ARG cc_start: 0.7582 (tmm-80) cc_final: 0.7236 (tmm-80) REVERT: B 914 ILE cc_start: 0.7745 (tt) cc_final: 0.7482 (tp) REVERT: B 924 LYS cc_start: 0.5873 (mptt) cc_final: 0.5457 (mppt) REVERT: B 932 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7199 (pmm) REVERT: B 934 ARG cc_start: 0.8113 (mtm180) cc_final: 0.7712 (ptt-90) outliers start: 36 outliers final: 24 residues processed: 166 average time/residue: 1.0140 time to fit residues: 184.0131 Evaluate side-chains 161 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 133 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 739 VAL Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 978 ILE 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 718 ARG Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain B residue 824 GLU 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 3 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 87 optimal weight: 0.0970 chunk 56 optimal weight: 0.3980 chunk 64 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.152826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.117939 restraints weight = 13403.286| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.32 r_work: 0.3271 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.4299 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= 0.200 Angle : 0.725 25.159 13808 Z= 0.339 Chirality : 0.070 2.151 1556 Planarity : 0.004 0.045 1741 Dihedral : 9.582 149.779 1395 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.94 % Favored : 95.82 % Rotamer: Outliers : 3.35 % Allowed : 31.74 % Favored : 64.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.24), residues: 1245 helix: 1.60 (0.20), residues: 683 sheet: -0.67 (0.44), residues: 130 loop : -0.75 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP A 938 HIS 0.004 0.001 HIS B 761 PHE 0.022 0.001 PHE B 664 TYR 0.016 0.001 TYR A 847 ARG 0.007 0.001 ARG B 875 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7650.28 seconds wall clock time: 136 minutes 6.89 seconds (8166.89 seconds total)