Starting phenix.real_space_refine on Wed Sep 17 17:09:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vpp_43412/09_2025/8vpp_43412_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vpp_43412/09_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_43412/09_2025/8vpp_43412.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vpp_43412/09_2025/8vpp_43412.map" model { file = "/net/cci-nas-00/data/ceres_data/8vpp_43412/09_2025/8vpp_43412_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vpp_43412/09_2025/8vpp_43412_trim.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'TPO:plan-1': 2, 'GLN:plan1': 3, 'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 2} 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: 2.51, per 1000 atoms: 0.25 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: 1.06 Conformation dependent library (CDL) restraints added in 438.8 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.38 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: 1.65 Time building geometry restraints manager: 1.33 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: 3.790 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.280 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:6.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.960 ------------------------------------------------------------------------------- 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 10165 Z= 0.204 Angle : 0.655 14.154 13812 Z= 0.344 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG A 918 TYR 0.012 0.001 TYR B 756 PHE 0.013 0.001 PHE A 535 TRP 0.044 0.001 TRP A 938 HIS 0.006 0.001 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00440 (10163) covalent geometry : angle 0.65400 (13808) SS BOND : bond 0.00384 ( 2) SS BOND : angle 1.82094 ( 4) hydrogen bonds : bond 0.17545 ( 537) hydrogen bonds : angle 5.97997 ( 1542) *********************** 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 : 0.371 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: 0.5119 time to fit residues: 157.1908 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 : 0.439 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 123 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 ASN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 257 ASN ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 ASN 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.155054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.120452 restraints weight = 13408.120| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.25 r_work: 0.3293 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10165 Z= 0.170 Angle : 0.799 22.915 13812 Z= 0.374 Chirality : 0.079 2.489 1556 Planarity : 0.005 0.060 1741 Dihedral : 10.484 146.147 1419 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.18 % Favored : 95.58 % Rotamer: Outliers : 7.46 % Allowed : 29.54 % Favored : 63.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.24), residues: 1245 helix: 1.41 (0.20), residues: 675 sheet: -1.82 (0.44), residues: 129 loop : -0.87 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 980 TYR 0.024 0.002 TYR A 847 PHE 0.024 0.002 PHE B 664 TRP 0.022 0.002 TRP A 938 HIS 0.006 0.001 HIS B 761 Details of bonding type rmsd covalent geometry : bond 0.00390 (10163) covalent geometry : angle 0.79804 (13808) SS BOND : bond 0.00454 ( 2) SS BOND : angle 1.99731 ( 4) hydrogen bonds : bond 0.05158 ( 537) hydrogen bonds : angle 4.84110 ( 1542) *********************** 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 250 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 172 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 SER cc_start: 0.8357 (t) cc_final: 0.8113 (m) REVERT: A 344 SER cc_start: 0.8757 (p) cc_final: 0.8430 (p) REVERT: A 345 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.7909 (pt) REVERT: A 368 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8371 (tt) REVERT: A 383 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8742 (mp) REVERT: A 590 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8238 (mp) REVERT: A 597 PHE cc_start: 0.7427 (t80) cc_final: 0.7154 (t80) REVERT: A 632 GLU cc_start: 0.7163 (pp20) cc_final: 0.6634 (pp20) REVERT: A 776 ARG cc_start: 0.7138 (ptm-80) cc_final: 0.6505 (ttp-110) REVERT: A 825 GLN cc_start: 0.7053 (OUTLIER) cc_final: 0.6812 (pm20) REVERT: A 874 GLU cc_start: 0.6173 (OUTLIER) cc_final: 0.5743 (mm-30) REVERT: A 944 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7609 (mp0) REVERT: A 957 ARG cc_start: 0.7880 (tpt170) cc_final: 0.7544 (tpt170) REVERT: B 731 ARG cc_start: 0.8649 (mtt-85) cc_final: 0.8363 (mtt-85) REVERT: B 909 ARG cc_start: 0.7511 (tmm-80) cc_final: 0.7229 (tmm-80) REVERT: B 932 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7366 (pmm) outliers start: 78 outliers final: 20 residues processed: 226 average time/residue: 0.4038 time to fit residues: 100.9967 Evaluate side-chains 169 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 944 GLU 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 16 optimal weight: 8.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.148652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.113464 restraints weight = 13618.237| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.27 r_work: 0.3210 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 10165 Z= 0.228 Angle : 0.792 23.385 13812 Z= 0.374 Chirality : 0.079 2.488 1556 Planarity : 0.005 0.048 1741 Dihedral : 10.043 144.820 1398 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.53 % Favored : 96.14 % Rotamer: Outliers : 6.98 % Allowed : 28.20 % Favored : 64.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.24), residues: 1245 helix: 1.12 (0.20), residues: 676 sheet: -1.51 (0.44), residues: 122 loop : -0.90 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 208 TYR 0.019 0.002 TYR B 756 PHE 0.024 0.002 PHE B 664 TRP 0.026 0.002 TRP A 938 HIS 0.006 0.001 HIS B 761 Details of bonding type rmsd covalent geometry : bond 0.00556 (10163) covalent geometry : angle 0.79174 (13808) SS BOND : bond 0.01007 ( 2) SS BOND : angle 1.64502 ( 4) hydrogen bonds : bond 0.05498 ( 537) hydrogen bonds : angle 4.78987 ( 1542) *********************** 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 224 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 151 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 92 PHE cc_start: 0.6911 (OUTLIER) cc_final: 0.6441 (p90) REVERT: A 154 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8741 (tp) REVERT: A 239 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7073 (mt-10) REVERT: A 336 ASP cc_start: 0.7895 (m-30) cc_final: 0.7443 (t0) REVERT: A 344 SER cc_start: 0.8801 (p) cc_final: 0.8470 (p) REVERT: A 345 ILE cc_start: 0.8489 (tt) cc_final: 0.8006 (pt) REVERT: A 364 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.7915 (ttpt) REVERT: A 383 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8731 (mp) REVERT: A 446 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8457 (ttt) REVERT: A 590 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8079 (mp) REVERT: A 597 PHE cc_start: 0.7607 (t80) cc_final: 0.7304 (t80) REVERT: A 621 ASN cc_start: 0.8990 (m110) cc_final: 0.8781 (m110) REVERT: A 632 GLU cc_start: 0.7257 (pp20) cc_final: 0.6826 (pp20) REVERT: A 874 GLU cc_start: 0.6073 (pm20) cc_final: 0.5607 (mm-30) REVERT: A 875 ARG cc_start: 0.5829 (OUTLIER) cc_final: 0.5425 (mtt90) REVERT: A 880 SER cc_start: 0.5685 (OUTLIER) cc_final: 0.5462 (p) REVERT: A 957 ARG cc_start: 0.7914 (tpt170) cc_final: 0.7704 (tpt170) REVERT: B 681 HIS cc_start: 0.2839 (OUTLIER) cc_final: 0.2550 (m-70) REVERT: B 731 ARG cc_start: 0.8722 (mtt-85) cc_final: 0.8365 (mtt-85) REVERT: B 776 ARG cc_start: 0.7961 (ttm-80) cc_final: 0.7646 (mtt-85) REVERT: B 859 LYS cc_start: 0.8677 (ttpp) cc_final: 0.8354 (tmmm) REVERT: B 879 ILE cc_start: 0.9279 (OUTLIER) cc_final: 0.8971 (mt) REVERT: B 932 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7363 (pmm) outliers start: 73 outliers final: 26 residues processed: 203 average time/residue: 0.4953 time to fit residues: 109.6356 Evaluate side-chains 174 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 137 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 154 LEU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 364 LYS Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 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 875 ARG Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 913 MET Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 818 THR 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 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 67 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 104 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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** B 869 ASN B 890 HIS B 998 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.150446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.115373 restraints weight = 13686.248| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.33 r_work: 0.3231 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 10165 Z= 0.152 Angle : 0.736 24.500 13812 Z= 0.344 Chirality : 0.072 2.249 1556 Planarity : 0.005 0.045 1741 Dihedral : 9.904 148.148 1398 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.69 % Favored : 96.06 % Rotamer: Outliers : 6.31 % Allowed : 28.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.24), residues: 1245 helix: 1.20 (0.20), residues: 683 sheet: -1.33 (0.43), residues: 128 loop : -0.92 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 875 TYR 0.019 0.002 TYR A 601 PHE 0.021 0.001 PHE B 664 TRP 0.035 0.001 TRP A 938 HIS 0.007 0.001 HIS A 636 Details of bonding type rmsd covalent geometry : bond 0.00361 (10163) covalent geometry : angle 0.73567 (13808) SS BOND : bond 0.00884 ( 2) SS BOND : angle 1.45392 ( 4) hydrogen bonds : bond 0.04603 ( 537) hydrogen bonds : angle 4.55721 ( 1542) *********************** 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 215 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 149 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 154 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8738 (tp) REVERT: A 239 GLU cc_start: 0.7658 (tm-30) cc_final: 0.6984 (mt-10) REVERT: A 336 ASP cc_start: 0.7873 (m-30) cc_final: 0.7392 (t0) REVERT: A 344 SER cc_start: 0.8757 (p) cc_final: 0.8444 (p) REVERT: A 345 ILE cc_start: 0.8427 (tt) cc_final: 0.7884 (pt) REVERT: A 383 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8699 (mp) REVERT: A 571 PHE cc_start: 0.8409 (t80) cc_final: 0.8124 (t80) REVERT: A 597 PHE cc_start: 0.7597 (t80) cc_final: 0.7328 (t80) REVERT: A 621 ASN cc_start: 0.8967 (m110) cc_final: 0.8719 (m110) REVERT: A 678 ILE cc_start: 0.7944 (mp) cc_final: 0.7625 (mm) REVERT: A 859 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7482 (ttmm) REVERT: A 875 ARG cc_start: 0.5841 (OUTLIER) cc_final: 0.5414 (mtt90) REVERT: A 880 SER cc_start: 0.5784 (OUTLIER) cc_final: 0.5551 (p) REVERT: B 681 HIS cc_start: 0.2986 (OUTLIER) cc_final: 0.2551 (m-70) REVERT: B 731 ARG cc_start: 0.8721 (mtt-85) cc_final: 0.8447 (mtt-85) REVERT: B 776 ARG cc_start: 0.7939 (ttm-80) cc_final: 0.7716 (mtt-85) REVERT: B 859 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8313 (tmmm) REVERT: B 867 GLN cc_start: 0.7075 (OUTLIER) cc_final: 0.6080 (tt0) REVERT: B 871 MET cc_start: 0.6880 (OUTLIER) cc_final: 0.6676 (mmm) REVERT: B 909 ARG cc_start: 0.7530 (tmm-80) cc_final: 0.7119 (tmm-80) REVERT: B 934 ARG cc_start: 0.8138 (mtm180) cc_final: 0.7759 (ptt-90) outliers start: 66 outliers final: 24 residues processed: 195 average time/residue: 0.5008 time to fit residues: 106.2726 Evaluate side-chains 172 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 154 LEU Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 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 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 913 MET 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 747 SER Chi-restraints excluded: chain B residue 859 LYS 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 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 102 optimal weight: 0.0970 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 16 optimal weight: 0.0050 chunk 54 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- 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** ** B 998 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 = 0.3781 r_free = 0.3781 target = 0.151507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.116858 restraints weight = 13635.867| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.32 r_work: 0.3262 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10165 Z= 0.136 Angle : 0.725 25.003 13812 Z= 0.335 Chirality : 0.070 2.177 1556 Planarity : 0.005 0.048 1741 Dihedral : 9.697 149.439 1395 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.86 % Favored : 95.90 % Rotamer: Outliers : 6.02 % Allowed : 28.59 % Favored : 65.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.24), residues: 1245 helix: 1.31 (0.20), residues: 686 sheet: -1.12 (0.44), residues: 126 loop : -0.87 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1008 TYR 0.014 0.001 TYR B 756 PHE 0.022 0.001 PHE B 664 TRP 0.038 0.001 TRP A 938 HIS 0.004 0.001 HIS A 636 Details of bonding type rmsd covalent geometry : bond 0.00321 (10163) covalent geometry : angle 0.72479 (13808) SS BOND : bond 0.00324 ( 2) SS BOND : angle 1.26790 ( 4) hydrogen bonds : bond 0.04312 ( 537) hydrogen bonds : angle 4.37725 ( 1542) *********************** 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 210 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 147 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 154 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8686 (tp) REVERT: A 156 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8858 (mt) REVERT: A 239 GLU cc_start: 0.7655 (tm-30) cc_final: 0.6976 (mt-10) REVERT: A 336 ASP cc_start: 0.7816 (m-30) cc_final: 0.7361 (t0) REVERT: A 344 SER cc_start: 0.8769 (p) cc_final: 0.8460 (p) REVERT: A 345 ILE cc_start: 0.8386 (tt) cc_final: 0.7800 (pt) REVERT: A 383 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8694 (mp) REVERT: A 597 PHE cc_start: 0.7553 (t80) cc_final: 0.7273 (t80) REVERT: A 621 ASN cc_start: 0.8970 (m110) cc_final: 0.8712 (m110) REVERT: A 875 ARG cc_start: 0.5901 (OUTLIER) cc_final: 0.5475 (mtt90) REVERT: A 880 SER cc_start: 0.5735 (OUTLIER) cc_final: 0.5488 (p) REVERT: A 900 GLN cc_start: 0.6819 (pp30) cc_final: 0.6573 (pp30) REVERT: B 681 HIS cc_start: 0.3102 (OUTLIER) cc_final: 0.2740 (m-70) REVERT: B 731 ARG cc_start: 0.8666 (mtt-85) cc_final: 0.8391 (mtt-85) REVERT: B 859 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8283 (tmmm) REVERT: B 867 GLN cc_start: 0.6916 (OUTLIER) cc_final: 0.5793 (tt0) REVERT: B 871 MET cc_start: 0.6857 (OUTLIER) cc_final: 0.6511 (mmm) REVERT: B 909 ARG cc_start: 0.7530 (tmm-80) cc_final: 0.7092 (tmm-80) REVERT: B 932 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7221 (pmm) REVERT: B 934 ARG cc_start: 0.8109 (mtm180) cc_final: 0.7722 (ptt-90) outliers start: 63 outliers final: 25 residues processed: 196 average time/residue: 0.4565 time to fit residues: 98.2225 Evaluate side-chains 178 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 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 388 ILE Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 875 ARG Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 718 ARG Chi-restraints excluded: chain B residue 859 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 109 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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** A1013 ASN B 998 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.148194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.113220 restraints weight = 13603.287| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.24 r_work: 0.3206 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 10165 Z= 0.205 Angle : 0.755 23.812 13812 Z= 0.356 Chirality : 0.076 2.393 1556 Planarity : 0.005 0.047 1741 Dihedral : 9.735 146.186 1395 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.02 % Favored : 95.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.24), residues: 1245 helix: 1.14 (0.20), residues: 685 sheet: -1.09 (0.43), residues: 125 loop : -0.82 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 875 TYR 0.018 0.002 TYR A 847 PHE 0.030 0.002 PHE B 664 TRP 0.038 0.002 TRP A 938 HIS 0.005 0.001 HIS A 636 Details of bonding type rmsd covalent geometry : bond 0.00506 (10163) covalent geometry : angle 0.75476 (13808) SS BOND : bond 0.00487 ( 2) SS BOND : angle 1.13512 ( 4) hydrogen bonds : bond 0.05043 ( 537) hydrogen bonds : angle 4.48019 ( 1542) *********************** 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 206 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 145 time to evaluate : 0.407 Fit side-chains REVERT: A 154 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8717 (tp) REVERT: A 156 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8889 (mt) REVERT: A 239 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7036 (mt-10) REVERT: A 336 ASP cc_start: 0.7881 (m-30) cc_final: 0.7437 (t0) REVERT: A 344 SER cc_start: 0.8823 (p) cc_final: 0.8530 (p) REVERT: A 383 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8714 (mp) REVERT: A 597 PHE cc_start: 0.7640 (t80) cc_final: 0.7339 (t80) REVERT: A 621 ASN cc_start: 0.8982 (m110) cc_final: 0.8722 (m110) REVERT: A 677 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8482 (mt) REVERT: A 859 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7583 (ttmm) REVERT: A 875 ARG cc_start: 0.5994 (OUTLIER) cc_final: 0.5475 (mtt90) REVERT: A 880 SER cc_start: 0.5859 (OUTLIER) cc_final: 0.5639 (p) REVERT: A 932 MET cc_start: 0.6367 (mmm) cc_final: 0.6123 (mmm) REVERT: B 637 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8427 (tp) REVERT: B 681 HIS cc_start: 0.3122 (OUTLIER) cc_final: 0.2697 (m-70) REVERT: B 731 ARG cc_start: 0.8711 (mtt-85) cc_final: 0.8410 (mtt-85) REVERT: B 867 GLN cc_start: 0.6984 (OUTLIER) cc_final: 0.5734 (tt0) REVERT: B 871 MET cc_start: 0.6857 (OUTLIER) cc_final: 0.6544 (mmm) REVERT: B 909 ARG cc_start: 0.7653 (tmm-80) cc_final: 0.7176 (tmm-80) REVERT: B 932 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7165 (pmm) REVERT: B 934 ARG cc_start: 0.8164 (mtm180) cc_final: 0.7790 (ptt-90) outliers start: 61 outliers final: 27 residues processed: 193 average time/residue: 0.4543 time to fit residues: 96.2348 Evaluate side-chains 176 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 137 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 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 677 LEU Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 859 LYS Chi-restraints excluded: chain A residue 860 ILE 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 975 THR Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain B residue 637 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 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 83 optimal weight: 0.7980 chunk 102 optimal weight: 0.0980 chunk 122 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 112 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 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 = 0.3776 r_free = 0.3776 target = 0.150893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.115863 restraints weight = 13541.514| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.35 r_work: 0.3243 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10165 Z= 0.143 Angle : 0.723 25.167 13812 Z= 0.336 Chirality : 0.070 2.182 1556 Planarity : 0.005 0.046 1741 Dihedral : 9.656 149.584 1395 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.78 % Favored : 95.98 % Rotamer: Outliers : 4.68 % Allowed : 30.21 % Favored : 65.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.24), residues: 1245 helix: 1.32 (0.20), residues: 687 sheet: -0.86 (0.43), residues: 126 loop : -0.79 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1008 TYR 0.015 0.001 TYR A 847 PHE 0.022 0.001 PHE B 664 TRP 0.040 0.001 TRP A 938 HIS 0.004 0.001 HIS B 761 Details of bonding type rmsd covalent geometry : bond 0.00341 (10163) covalent geometry : angle 0.72269 (13808) SS BOND : bond 0.00387 ( 2) SS BOND : angle 1.50340 ( 4) hydrogen bonds : bond 0.04365 ( 537) hydrogen bonds : angle 4.33979 ( 1542) *********************** 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 196 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 147 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 CYS cc_start: 0.6888 (t) cc_final: 0.6072 (m) REVERT: A 156 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8877 (mt) REVERT: A 239 GLU cc_start: 0.7642 (tm-30) cc_final: 0.6985 (mt-10) REVERT: A 336 ASP cc_start: 0.7815 (m-30) cc_final: 0.7292 (t0) REVERT: A 344 SER cc_start: 0.8779 (p) cc_final: 0.8502 (p) REVERT: A 383 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8707 (mp) REVERT: A 597 PHE cc_start: 0.7561 (t80) cc_final: 0.7299 (t80) REVERT: A 621 ASN cc_start: 0.8980 (m110) cc_final: 0.8712 (m110) REVERT: A 677 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8426 (mt) REVERT: A 880 SER cc_start: 0.5867 (OUTLIER) cc_final: 0.5666 (p) REVERT: A 900 GLN cc_start: 0.6648 (pp30) cc_final: 0.6368 (pp30) REVERT: A 932 MET cc_start: 0.6334 (mmm) cc_final: 0.6034 (mtm) REVERT: B 681 HIS cc_start: 0.3203 (OUTLIER) cc_final: 0.2781 (m-70) REVERT: B 718 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7631 (mtt-85) REVERT: B 731 ARG cc_start: 0.8636 (mtt-85) cc_final: 0.8362 (mtt-85) REVERT: B 867 GLN cc_start: 0.6746 (OUTLIER) cc_final: 0.6398 (tm-30) REVERT: B 871 MET cc_start: 0.6819 (OUTLIER) cc_final: 0.6406 (mmm) REVERT: B 932 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7203 (pmm) REVERT: B 934 ARG cc_start: 0.8190 (mtm180) cc_final: 0.7830 (ptt-90) outliers start: 49 outliers final: 26 residues processed: 185 average time/residue: 0.5088 time to fit residues: 102.3025 Evaluate side-chains 173 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 875 ARG Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1013 ASN Chi-restraints excluded: chain A residue 1015 LEU Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 718 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 116 optimal weight: 0.4980 chunk 91 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 890 HIS A1013 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.149526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.114738 restraints weight = 13453.364| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.24 r_work: 0.3228 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10165 Z= 0.170 Angle : 0.747 24.662 13812 Z= 0.350 Chirality : 0.073 2.261 1556 Planarity : 0.005 0.046 1741 Dihedral : 9.671 148.196 1395 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.94 % Favored : 95.82 % Rotamer: Outliers : 4.40 % Allowed : 30.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.24), residues: 1245 helix: 1.32 (0.20), residues: 686 sheet: -0.76 (0.43), residues: 126 loop : -0.75 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1008 TYR 0.020 0.002 TYR A 601 PHE 0.026 0.001 PHE B 664 TRP 0.042 0.001 TRP A 938 HIS 0.006 0.001 HIS A 890 Details of bonding type rmsd covalent geometry : bond 0.00416 (10163) covalent geometry : angle 0.74693 (13808) SS BOND : bond 0.00575 ( 2) SS BOND : angle 1.62417 ( 4) hydrogen bonds : bond 0.04624 ( 537) hydrogen bonds : angle 4.39475 ( 1542) *********************** 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 190 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 144 time to evaluate : 0.404 Fit side-chains REVERT: A 239 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7025 (mt-10) REVERT: A 257 ASN cc_start: 0.7881 (p0) cc_final: 0.7484 (t0) REVERT: A 336 ASP cc_start: 0.7865 (m-30) cc_final: 0.7299 (t0) REVERT: A 344 SER cc_start: 0.8821 (p) cc_final: 0.8511 (p) REVERT: A 345 ILE cc_start: 0.8407 (tt) cc_final: 0.7895 (pt) REVERT: A 383 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8684 (mp) REVERT: A 590 ILE cc_start: 0.8381 (mp) cc_final: 0.8047 (mp) REVERT: A 597 PHE cc_start: 0.7510 (t80) cc_final: 0.7261 (t80) REVERT: A 606 LYS cc_start: 0.8867 (tppp) cc_final: 0.7761 (mppt) REVERT: A 621 ASN cc_start: 0.8983 (m110) cc_final: 0.8715 (m110) REVERT: A 677 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8464 (mt) REVERT: A 875 ARG cc_start: 0.6151 (OUTLIER) cc_final: 0.5326 (mtt90) REVERT: A 900 GLN cc_start: 0.6923 (pp30) cc_final: 0.6564 (pp30) REVERT: A 932 MET cc_start: 0.6239 (mmm) cc_final: 0.5972 (mtm) REVERT: A 967 ARG cc_start: 0.6988 (ttp-110) cc_final: 0.6749 (mtp85) REVERT: B 637 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8442 (tp) REVERT: B 681 HIS cc_start: 0.3325 (OUTLIER) cc_final: 0.2836 (m-70) REVERT: B 718 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7684 (mtt-85) REVERT: B 731 ARG cc_start: 0.8667 (mtt-85) cc_final: 0.8375 (mtt-85) REVERT: B 867 GLN cc_start: 0.6899 (OUTLIER) cc_final: 0.6599 (tm-30) REVERT: B 871 MET cc_start: 0.6814 (OUTLIER) cc_final: 0.6468 (mmm) REVERT: B 911 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8365 (mp0) REVERT: B 932 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7210 (pmm) REVERT: B 934 ARG cc_start: 0.8149 (mtm180) cc_final: 0.7812 (ptt-90) outliers start: 46 outliers final: 26 residues processed: 180 average time/residue: 0.4891 time to fit residues: 96.0627 Evaluate side-chains 173 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 820 ILE 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 637 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 19 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 114 optimal weight: 0.4980 chunk 92 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 91 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 ASN ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3774 r_free = 0.3774 target = 0.150864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.115948 restraints weight = 13398.394| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.32 r_work: 0.3242 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10165 Z= 0.143 Angle : 0.732 25.131 13812 Z= 0.342 Chirality : 0.070 2.182 1556 Planarity : 0.005 0.046 1741 Dihedral : 9.626 149.447 1395 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.94 % Favored : 95.82 % Rotamer: Outliers : 4.30 % Allowed : 30.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.24), residues: 1245 helix: 1.44 (0.20), residues: 686 sheet: -0.67 (0.44), residues: 126 loop : -0.73 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1008 TYR 0.015 0.001 TYR A 847 PHE 0.024 0.001 PHE B 664 TRP 0.044 0.001 TRP A 938 HIS 0.004 0.001 HIS A 636 Details of bonding type rmsd covalent geometry : bond 0.00337 (10163) covalent geometry : angle 0.73154 (13808) SS BOND : bond 0.00362 ( 2) SS BOND : angle 1.40042 ( 4) hydrogen bonds : bond 0.04326 ( 537) hydrogen bonds : angle 4.33158 ( 1542) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 145 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 52 CYS cc_start: 0.6563 (t) cc_final: 0.5835 (m) REVERT: A 239 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7005 (mt-10) REVERT: A 257 ASN cc_start: 0.7824 (p0) cc_final: 0.7440 (t0) REVERT: A 336 ASP cc_start: 0.7816 (m-30) cc_final: 0.7223 (t0) REVERT: A 344 SER cc_start: 0.8813 (p) cc_final: 0.8503 (p) REVERT: A 345 ILE cc_start: 0.8395 (tt) cc_final: 0.7872 (pt) REVERT: A 383 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8697 (mp) REVERT: A 590 ILE cc_start: 0.8332 (mp) cc_final: 0.7974 (mp) REVERT: A 597 PHE cc_start: 0.7561 (t80) cc_final: 0.7323 (t80) REVERT: A 606 LYS cc_start: 0.8859 (tppp) cc_final: 0.7726 (mppt) REVERT: A 621 ASN cc_start: 0.8957 (m110) cc_final: 0.8672 (m110) REVERT: A 900 GLN cc_start: 0.6835 (pp30) cc_final: 0.6427 (pp30) REVERT: A 932 MET cc_start: 0.6269 (mmm) cc_final: 0.5987 (mtm) REVERT: A 967 ARG cc_start: 0.6964 (ttp-110) cc_final: 0.6722 (mtp85) REVERT: B 643 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.6625 (mm-40) REVERT: B 681 HIS cc_start: 0.3446 (OUTLIER) cc_final: 0.3170 (m-70) REVERT: B 718 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7616 (mmt-90) REVERT: B 731 ARG cc_start: 0.8620 (mtt-85) cc_final: 0.8339 (mtt-85) REVERT: B 867 GLN cc_start: 0.6792 (OUTLIER) cc_final: 0.6417 (tm-30) REVERT: B 871 MET cc_start: 0.6779 (OUTLIER) cc_final: 0.6263 (mmm) REVERT: B 909 ARG cc_start: 0.7365 (tmm-80) cc_final: 0.7068 (tmm-80) REVERT: B 911 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8331 (mp0) REVERT: B 924 LYS cc_start: 0.5920 (mptt) cc_final: 0.5468 (mppt) REVERT: B 932 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7204 (pmm) REVERT: B 934 ARG cc_start: 0.8159 (mtm180) cc_final: 0.7766 (ptt-90) outliers start: 45 outliers final: 26 residues processed: 177 average time/residue: 0.4975 time to fit residues: 95.7795 Evaluate side-chains 170 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 0.468 ------------------------------------------------------------------------------- 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 526 THR 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 820 ILE 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 1013 ASN Chi-restraints excluded: chain B residue 643 GLN Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 718 ARG Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain B residue 867 GLN Chi-restraints excluded: chain B residue 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 45 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 91 optimal weight: 0.6980 chunk 52 optimal weight: 0.1980 chunk 4 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 3 optimal weight: 0.3980 chunk 37 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 744 ASN A 767 ASN A1013 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.151863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.117013 restraints weight = 13321.773| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.31 r_work: 0.3263 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10165 Z= 0.136 Angle : 0.741 25.190 13812 Z= 0.347 Chirality : 0.070 2.142 1556 Planarity : 0.004 0.046 1741 Dihedral : 9.619 149.893 1395 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.94 % Favored : 95.82 % Rotamer: Outliers : 3.54 % Allowed : 31.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.24), residues: 1245 helix: 1.49 (0.20), residues: 686 sheet: -0.62 (0.44), residues: 126 loop : -0.69 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1008 TYR 0.015 0.001 TYR A 155 PHE 0.021 0.001 PHE B 664 TRP 0.044 0.001 TRP A 938 HIS 0.006 0.001 HIS A 636 Details of bonding type rmsd covalent geometry : bond 0.00316 (10163) covalent geometry : angle 0.74108 (13808) SS BOND : bond 0.00309 ( 2) SS BOND : angle 1.16016 ( 4) hydrogen bonds : bond 0.04206 ( 537) hydrogen bonds : angle 4.31409 ( 1542) ********************** 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 175 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 239 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7017 (mt-10) REVERT: A 257 ASN cc_start: 0.7857 (p0) cc_final: 0.7504 (t0) REVERT: A 336 ASP cc_start: 0.7802 (m-30) cc_final: 0.7357 (t0) REVERT: A 344 SER cc_start: 0.8806 (p) cc_final: 0.8495 (p) REVERT: A 345 ILE cc_start: 0.8366 (tt) cc_final: 0.7841 (pt) REVERT: A 383 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8690 (mp) REVERT: A 590 ILE cc_start: 0.8265 (mp) cc_final: 0.7879 (mp) REVERT: A 606 LYS cc_start: 0.8836 (tppp) cc_final: 0.7708 (mppt) REVERT: A 621 ASN cc_start: 0.8972 (m110) cc_final: 0.8698 (m110) REVERT: A 932 MET cc_start: 0.6219 (mmm) cc_final: 0.5954 (mtm) REVERT: A 967 ARG cc_start: 0.6998 (ttp-110) cc_final: 0.6755 (mtp85) REVERT: A 986 SER cc_start: 0.7714 (OUTLIER) cc_final: 0.7293 (t) REVERT: B 643 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.6548 (mm-40) REVERT: B 681 HIS cc_start: 0.3370 (OUTLIER) cc_final: 0.3150 (m-70) REVERT: B 731 ARG cc_start: 0.8606 (mtt-85) cc_final: 0.8354 (mtt-85) REVERT: B 911 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8332 (mp0) REVERT: B 924 LYS cc_start: 0.5892 (mptt) cc_final: 0.5485 (mppt) REVERT: B 932 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7145 (pmm) REVERT: B 934 ARG cc_start: 0.8098 (mtm180) cc_final: 0.7723 (ptt-90) outliers start: 37 outliers final: 26 residues processed: 167 average time/residue: 0.4649 time to fit residues: 84.6369 Evaluate side-chains 164 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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 526 THR Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 820 ILE 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 1013 ASN Chi-restraints excluded: chain B residue 643 GLN Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain B residue 880 SER Chi-restraints excluded: chain B residue 895 LEU Chi-restraints excluded: chain B residue 925 ASP Chi-restraints excluded: chain B residue 932 MET Chi-restraints excluded: chain B residue 963 LEU 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 33 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 ASN ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 767 ASN A 906 HIS A1013 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.151041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.116127 restraints weight = 13488.501| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.32 r_work: 0.3239 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10165 Z= 0.158 Angle : 0.752 25.281 13812 Z= 0.354 Chirality : 0.071 2.170 1556 Planarity : 0.005 0.047 1741 Dihedral : 9.621 149.666 1395 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.94 % Favored : 95.82 % Rotamer: Outliers : 3.92 % Allowed : 31.74 % Favored : 64.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.24), residues: 1245 helix: 1.47 (0.20), residues: 686 sheet: -0.58 (0.44), residues: 125 loop : -0.69 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1008 TYR 0.017 0.001 TYR A 847 PHE 0.023 0.001 PHE B 664 TRP 0.043 0.001 TRP A 938 HIS 0.004 0.001 HIS B 761 Details of bonding type rmsd covalent geometry : bond 0.00377 (10163) covalent geometry : angle 0.75137 (13808) SS BOND : bond 0.00570 ( 2) SS BOND : angle 1.84826 ( 4) hydrogen bonds : bond 0.04352 ( 537) hydrogen bonds : angle 4.32547 ( 1542) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4112.61 seconds wall clock time: 70 minutes 56.96 seconds (4256.96 seconds total)