Starting phenix.real_space_refine on Sat Dec 28 11:27:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zz6_15036/12_2024/7zz6_15036.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zz6_15036/12_2024/7zz6_15036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zz6_15036/12_2024/7zz6_15036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zz6_15036/12_2024/7zz6_15036.map" model { file = "/net/cci-nas-00/data/ceres_data/7zz6_15036/12_2024/7zz6_15036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zz6_15036/12_2024/7zz6_15036.cif" } resolution = 2.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 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 Mn 2 7.51 5 Mg 2 5.21 5 S 36 5.16 5 C 5148 2.51 5 N 1367 2.21 5 O 1702 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8257 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 4047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 4047 Classifications: {'peptide': 509} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 485} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 4037 Classifications: {'peptide': 508} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 484} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 8 Unusual residues: {' MG': 1, ' MN': 1, 'PYR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 8 Unusual residues: {' MG': 1, ' MN': 1, 'PYR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 99 Classifications: {'water': 99} Link IDs: {None: 98} Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Time building chain proxies: 5.59, per 1000 atoms: 0.68 Number of scatterers: 8257 At special positions: 0 Unit cell: (96.46, 71.02, 110.24, 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) Mn 2 24.99 S 36 16.00 Mg 2 11.99 O 1702 8.00 N 1367 7.00 C 5148 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.53 Conformation dependent library (CDL) restraints added in 945.0 milliseconds 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1894 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 2 sheets defined 62.1% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'D' and resid 502 through 511 Processing helix chain 'D' and resid 511 through 522 Processing helix chain 'D' and resid 533 through 540 Processing helix chain 'D' and resid 545 through 560 removed outlier: 3.709A pdb=" N GLY D 551 " --> pdb=" O GLN D 547 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE D 552 " --> pdb=" O ASP D 548 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLN D 554 " --> pdb=" O LYS D 550 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ALA D 555 " --> pdb=" O GLY D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 580 removed outlier: 3.712A pdb=" N TYR D 578 " --> pdb=" O PHE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 596 Processing helix chain 'D' and resid 617 through 631 Processing helix chain 'D' and resid 645 through 658 removed outlier: 4.723A pdb=" N LYS D 650 " --> pdb=" O PRO D 646 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N SER D 651 " --> pdb=" O GLN D 647 " (cutoff:3.500A) Processing helix chain 'D' and resid 681 through 695 Processing helix chain 'D' and resid 710 through 725 Processing helix chain 'D' and resid 739 through 751 Processing helix chain 'D' and resid 759 through 763 Processing helix chain 'D' and resid 770 through 778 Processing helix chain 'D' and resid 788 through 804 removed outlier: 3.640A pdb=" N HIS D 797 " --> pdb=" O GLU D 793 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR D 798 " --> pdb=" O GLN D 794 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS D 804 " --> pdb=" O GLU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 805 through 810 Proline residue: D 808 - end of helix No H-bonds generated for 'chain 'D' and resid 805 through 810' Processing helix chain 'D' and resid 817 through 822 removed outlier: 3.572A pdb=" N VAL D 820 " --> pdb=" O GLN D 817 " (cutoff:3.500A) Processing helix chain 'D' and resid 826 through 841 Processing helix chain 'D' and resid 842 through 844 No H-bonds generated for 'chain 'D' and resid 842 through 844' Processing helix chain 'D' and resid 845 through 860 Processing helix chain 'D' and resid 868 through 883 removed outlier: 3.565A pdb=" N VAL D 872 " --> pdb=" O PRO D 868 " (cutoff:3.500A) Processing helix chain 'D' and resid 886 through 893 Processing helix chain 'D' and resid 894 through 897 Processing helix chain 'D' and resid 900 through 908 Processing helix chain 'D' and resid 919 through 927 Processing helix chain 'D' and resid 936 through 941 Processing helix chain 'D' and resid 945 through 957 Processing helix chain 'D' and resid 962 through 972 Processing helix chain 'D' and resid 972 through 987 Processing helix chain 'D' and resid 988 through 992 Processing helix chain 'A' and resid 502 through 511 Processing helix chain 'A' and resid 511 through 522 Processing helix chain 'A' and resid 533 through 540 Processing helix chain 'A' and resid 545 through 560 removed outlier: 3.698A pdb=" N GLY A 551 " --> pdb=" O GLN A 547 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE A 552 " --> pdb=" O ASP A 548 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLN A 554 " --> pdb=" O LYS A 550 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ALA A 555 " --> pdb=" O GLY A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 580 removed outlier: 3.776A pdb=" N TYR A 578 " --> pdb=" O PHE A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 596 Processing helix chain 'A' and resid 617 through 632 Processing helix chain 'A' and resid 645 through 658 removed outlier: 4.628A pdb=" N LYS A 650 " --> pdb=" O PRO A 646 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N SER A 651 " --> pdb=" O GLN A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 695 Processing helix chain 'A' and resid 710 through 723 Processing helix chain 'A' and resid 739 through 751 Processing helix chain 'A' and resid 759 through 763 Processing helix chain 'A' and resid 770 through 778 Processing helix chain 'A' and resid 788 through 804 removed outlier: 3.626A pdb=" N HIS A 797 " --> pdb=" O GLU A 793 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR A 798 " --> pdb=" O GLN A 794 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS A 804 " --> pdb=" O GLU A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 810 Proline residue: A 808 - end of helix No H-bonds generated for 'chain 'A' and resid 805 through 810' Processing helix chain 'A' and resid 817 through 822 removed outlier: 3.621A pdb=" N VAL A 820 " --> pdb=" O GLN A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 839 Processing helix chain 'A' and resid 840 through 841 No H-bonds generated for 'chain 'A' and resid 840 through 841' Processing helix chain 'A' and resid 842 through 844 No H-bonds generated for 'chain 'A' and resid 842 through 844' Processing helix chain 'A' and resid 845 through 861 Processing helix chain 'A' and resid 868 through 883 removed outlier: 3.594A pdb=" N VAL A 872 " --> pdb=" O PRO A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 893 Processing helix chain 'A' and resid 894 through 896 No H-bonds generated for 'chain 'A' and resid 894 through 896' Processing helix chain 'A' and resid 900 through 908 Processing helix chain 'A' and resid 919 through 928 Processing helix chain 'A' and resid 936 through 941 Processing helix chain 'A' and resid 945 through 957 Processing helix chain 'A' and resid 962 through 972 Processing helix chain 'A' and resid 972 through 987 Processing helix chain 'A' and resid 988 through 992 Processing sheet with id=AA1, first strand: chain 'D' and resid 526 through 529 removed outlier: 6.818A pdb=" N LEU D 527 " --> pdb=" O SER D 565 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N GLU D 567 " --> pdb=" O LEU D 527 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASP D 529 " --> pdb=" O GLU D 567 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N TRP D 569 " --> pdb=" O ASP D 529 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ALA D 566 " --> pdb=" O GLN D 602 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LEU D 604 " --> pdb=" O ALA D 566 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N MET D 568 " --> pdb=" O LEU D 604 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N THR D 733 " --> pdb=" O ASP D 756 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU D 526 " --> pdb=" O ILE D 755 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL D 757 " --> pdb=" O LEU D 526 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N THR D 528 " --> pdb=" O VAL D 757 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 526 through 529 removed outlier: 6.835A pdb=" N LEU A 527 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N GLU A 567 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASP A 529 " --> pdb=" O GLU A 567 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N TRP A 569 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ALA A 566 " --> pdb=" O GLN A 602 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N LEU A 604 " --> pdb=" O ALA A 566 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N MET A 568 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N THR A 733 " --> pdb=" O ASP A 756 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU A 526 " --> pdb=" O ILE A 755 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL A 757 " --> pdb=" O LEU A 526 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N THR A 528 " --> pdb=" O VAL A 757 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1191 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.47 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2694 1.34 - 1.46: 1840 1.46 - 1.58: 3665 1.58 - 1.70: 0 1.70 - 1.82: 70 Bond restraints: 8269 Sorted by residual: bond pdb=" C1 PYR A1203 " pdb=" C2 PYR A1203 " ideal model delta sigma weight residual 1.558 1.389 0.169 2.00e-02 2.50e+03 7.15e+01 bond pdb=" C1 PYR D1203 " pdb=" C2 PYR D1203 " ideal model delta sigma weight residual 1.558 1.393 0.165 2.00e-02 2.50e+03 6.84e+01 bond pdb=" C2 PYR A1203 " pdb=" O3 PYR A1203 " ideal model delta sigma weight residual 1.210 1.309 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" C2 PYR D1203 " pdb=" O3 PYR D1203 " ideal model delta sigma weight residual 1.210 1.308 -0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" NZ KCX A 703 " pdb=" CX KCX A 703 " ideal model delta sigma weight residual 1.411 1.324 0.087 2.00e-02 2.50e+03 1.91e+01 ... (remaining 8264 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 11066 2.51 - 5.03: 109 5.03 - 7.54: 11 7.54 - 10.05: 6 10.05 - 12.57: 1 Bond angle restraints: 11193 Sorted by residual: angle pdb=" CB MET D 858 " pdb=" CG MET D 858 " pdb=" SD MET D 858 " ideal model delta sigma weight residual 112.70 125.27 -12.57 3.00e+00 1.11e-01 1.75e+01 angle pdb=" CB MET D 982 " pdb=" CG MET D 982 " pdb=" SD MET D 982 " ideal model delta sigma weight residual 112.70 122.56 -9.86 3.00e+00 1.11e-01 1.08e+01 angle pdb=" O1 PYR D1203 " pdb=" C1 PYR D1203 " pdb=" O2 PYR D1203 " ideal model delta sigma weight residual 129.19 119.71 9.48 3.00e+00 1.11e-01 9.98e+00 angle pdb=" O1 PYR A1203 " pdb=" C1 PYR A1203 " pdb=" O2 PYR A1203 " ideal model delta sigma weight residual 129.19 120.00 9.19 3.00e+00 1.11e-01 9.39e+00 angle pdb=" CB MET A 568 " pdb=" CG MET A 568 " pdb=" SD MET A 568 " ideal model delta sigma weight residual 112.70 121.75 -9.05 3.00e+00 1.11e-01 9.11e+00 ... (remaining 11188 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 4355 17.86 - 35.72: 443 35.72 - 53.58: 132 53.58 - 71.44: 32 71.44 - 89.30: 21 Dihedral angle restraints: 4983 sinusoidal: 2026 harmonic: 2957 Sorted by residual: dihedral pdb=" CA ASP A 929 " pdb=" C ASP A 929 " pdb=" N LYS A 930 " pdb=" CA LYS A 930 " ideal model delta harmonic sigma weight residual 180.00 -156.71 -23.29 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA LEU D 778 " pdb=" C LEU D 778 " pdb=" N GLU D 779 " pdb=" CA GLU D 779 " ideal model delta harmonic sigma weight residual -180.00 -161.43 -18.57 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA LEU A 778 " pdb=" C LEU A 778 " pdb=" N GLU A 779 " pdb=" CA GLU A 779 " ideal model delta harmonic sigma weight residual -180.00 -162.03 -17.97 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 4980 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 596 0.029 - 0.057: 385 0.057 - 0.086: 162 0.086 - 0.114: 66 0.114 - 0.143: 12 Chirality restraints: 1221 Sorted by residual: chirality pdb=" CA VAL A 866 " pdb=" N VAL A 866 " pdb=" C VAL A 866 " pdb=" CB VAL A 866 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CA VAL D 866 " pdb=" N VAL D 866 " pdb=" C VAL D 866 " pdb=" CB VAL D 866 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA ILE D 666 " pdb=" N ILE D 666 " pdb=" C ILE D 666 " pdb=" CB ILE D 666 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01 ... (remaining 1218 not shown) Planarity restraints: 1466 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG D 533 " 0.007 2.00e-02 2.50e+03 1.44e-02 2.09e+00 pdb=" C ARG D 533 " -0.025 2.00e-02 2.50e+03 pdb=" O ARG D 533 " 0.009 2.00e-02 2.50e+03 pdb=" N ASP D 534 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 533 " -0.007 2.00e-02 2.50e+03 1.42e-02 2.01e+00 pdb=" C ARG A 533 " 0.025 2.00e-02 2.50e+03 pdb=" O ARG A 533 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP A 534 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 867 " -0.021 5.00e-02 4.00e+02 3.15e-02 1.59e+00 pdb=" N PRO D 868 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 868 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 868 " -0.016 5.00e-02 4.00e+02 ... (remaining 1463 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.09: 3 2.09 - 2.79: 2245 2.79 - 3.49: 12466 3.49 - 4.20: 22577 4.20 - 4.90: 37839 Nonbonded interactions: 75130 Sorted by model distance: nonbonded pdb=" OD1 ASP A 753 " pdb="MG MG A1201 " model vdw 1.385 2.170 nonbonded pdb=" NE2 HIS A 732 " pdb="MN MN A1202 " model vdw 1.835 2.400 nonbonded pdb=" NE2 HIS D 732 " pdb="MN MN D1202 " model vdw 1.838 2.400 nonbonded pdb=" OD1 ASP A 753 " pdb=" O HOH A1301 " model vdw 2.143 3.040 nonbonded pdb="MN MN D1202 " pdb=" O HOH D1335 " model vdw 2.193 2.320 ... (remaining 75125 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'D' and (resid 487 through 994 or resid 1201 through 1203)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.560 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 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 : 0.006 0.169 8269 Z= 0.422 Angle : 0.682 12.566 11193 Z= 0.359 Chirality : 0.045 0.143 1221 Planarity : 0.003 0.032 1466 Dihedral : 17.300 89.298 3089 Min Nonbonded Distance : 1.385 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.48 % Allowed : 15.91 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.26), residues: 1007 helix: 1.07 (0.22), residues: 530 sheet: -0.96 (0.47), residues: 86 loop : 0.02 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 586 HIS 0.005 0.001 HIS D 732 PHE 0.013 0.002 PHE D 907 TYR 0.011 0.002 TYR D 853 ARG 0.004 0.000 ARG D 845 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 48 time to evaluate : 1.032 Fit side-chains outliers start: 30 outliers final: 26 residues processed: 75 average time/residue: 1.0371 time to fit residues: 84.5522 Evaluate side-chains 73 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 47 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 500 LYS Chi-restraints excluded: chain D residue 569 TRP Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 757 VAL Chi-restraints excluded: chain D residue 770 SER Chi-restraints excluded: chain D residue 814 THR Chi-restraints excluded: chain D residue 849 ILE Chi-restraints excluded: chain D residue 883 ASN Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 928 LYS Chi-restraints excluded: chain D residue 934 THR Chi-restraints excluded: chain D residue 948 THR Chi-restraints excluded: chain D residue 967 ILE Chi-restraints excluded: chain D residue 982 MET Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 609 ASN Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 770 SER Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 948 THR Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain A residue 993 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 0.0970 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 829 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8269 Z= 0.188 Angle : 0.511 6.291 11193 Z= 0.274 Chirality : 0.041 0.153 1221 Planarity : 0.004 0.033 1466 Dihedral : 6.875 51.941 1165 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.02 % Allowed : 14.75 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.27), residues: 1007 helix: 1.29 (0.22), residues: 546 sheet: -0.89 (0.49), residues: 86 loop : 0.24 (0.34), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 644 HIS 0.004 0.001 HIS D 732 PHE 0.012 0.001 PHE D 879 TYR 0.008 0.001 TYR A 806 ARG 0.002 0.000 ARG D 845 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 51 time to evaluate : 0.998 Fit side-chains outliers start: 26 outliers final: 10 residues processed: 71 average time/residue: 1.2185 time to fit residues: 93.3445 Evaluate side-chains 58 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 569 TRP Chi-restraints excluded: chain D residue 705 MET Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 967 ILE Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 609 ASN Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain A residue 993 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 0.6980 chunk 28 optimal weight: 0.0040 chunk 75 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 882 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8269 Z= 0.175 Angle : 0.496 5.497 11193 Z= 0.263 Chirality : 0.040 0.151 1221 Planarity : 0.004 0.037 1466 Dihedral : 6.181 52.388 1136 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.67 % Allowed : 14.75 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.27), residues: 1007 helix: 1.44 (0.23), residues: 546 sheet: -0.87 (0.50), residues: 86 loop : 0.26 (0.34), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 569 HIS 0.004 0.001 HIS D 732 PHE 0.011 0.001 PHE D 879 TYR 0.009 0.001 TYR D 853 ARG 0.002 0.000 ARG D 845 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 50 time to evaluate : 1.027 Fit side-chains REVERT: A 845 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7089 (ptm160) outliers start: 23 outliers final: 12 residues processed: 68 average time/residue: 1.0841 time to fit residues: 80.0072 Evaluate side-chains 58 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 569 TRP Chi-restraints excluded: chain D residue 609 ASN Chi-restraints excluded: chain D residue 705 MET Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 849 ILE Chi-restraints excluded: chain D residue 967 ILE Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 609 ASN Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 845 ARG Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain A residue 993 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 80 optimal weight: 0.4980 chunk 54 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8269 Z= 0.268 Angle : 0.545 7.877 11193 Z= 0.290 Chirality : 0.042 0.151 1221 Planarity : 0.004 0.038 1466 Dihedral : 6.460 51.630 1136 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.25 % Allowed : 13.94 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.27), residues: 1007 helix: 1.46 (0.22), residues: 544 sheet: -0.95 (0.50), residues: 86 loop : 0.12 (0.34), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 799 HIS 0.005 0.001 HIS A 536 PHE 0.013 0.001 PHE D 879 TYR 0.010 0.001 TYR D 685 ARG 0.003 0.000 ARG A 593 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 47 time to evaluate : 0.976 Fit side-chains REVERT: A 845 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7196 (ptm160) REVERT: A 893 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7738 (ttt90) outliers start: 28 outliers final: 14 residues processed: 70 average time/residue: 1.1408 time to fit residues: 86.4583 Evaluate side-chains 62 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 569 TRP Chi-restraints excluded: chain D residue 609 ASN Chi-restraints excluded: chain D residue 705 MET Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 849 ILE Chi-restraints excluded: chain D residue 967 ILE Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 609 ASN Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 845 ARG Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 893 ARG Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain A residue 993 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 82 optimal weight: 0.0030 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 87 optimal weight: 0.4980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8269 Z= 0.180 Angle : 0.509 8.454 11193 Z= 0.266 Chirality : 0.041 0.151 1221 Planarity : 0.004 0.038 1466 Dihedral : 6.170 51.676 1136 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.67 % Allowed : 14.29 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.27), residues: 1007 helix: 1.52 (0.23), residues: 545 sheet: -0.92 (0.51), residues: 86 loop : 0.20 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 569 HIS 0.004 0.001 HIS D 732 PHE 0.012 0.001 PHE D 879 TYR 0.009 0.001 TYR D 853 ARG 0.001 0.000 ARG D 593 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 49 time to evaluate : 1.041 Fit side-chains outliers start: 23 outliers final: 13 residues processed: 64 average time/residue: 1.1016 time to fit residues: 76.5762 Evaluate side-chains 59 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 569 TRP Chi-restraints excluded: chain D residue 609 ASN Chi-restraints excluded: chain D residue 705 MET Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 849 ILE Chi-restraints excluded: chain D residue 967 ILE Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 609 ASN Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 967 ILE Chi-restraints excluded: chain A residue 993 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 0.1980 chunk 23 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 chunk 32 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8269 Z= 0.191 Angle : 0.513 8.810 11193 Z= 0.268 Chirality : 0.041 0.150 1221 Planarity : 0.004 0.038 1466 Dihedral : 6.087 51.338 1135 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.44 % Allowed : 14.52 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.27), residues: 1007 helix: 1.61 (0.23), residues: 546 sheet: -0.92 (0.51), residues: 86 loop : 0.20 (0.34), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 799 HIS 0.004 0.001 HIS A 536 PHE 0.012 0.001 PHE D 879 TYR 0.008 0.001 TYR D 685 ARG 0.002 0.000 ARG A 593 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 52 time to evaluate : 0.770 Fit side-chains REVERT: A 845 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.7029 (ptm160) outliers start: 21 outliers final: 12 residues processed: 68 average time/residue: 1.0883 time to fit residues: 80.1394 Evaluate side-chains 61 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 569 TRP Chi-restraints excluded: chain D residue 609 ASN Chi-restraints excluded: chain D residue 705 MET Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 849 ILE Chi-restraints excluded: chain D residue 967 ILE Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 609 ASN Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 845 ARG Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 967 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 59 optimal weight: 0.2980 chunk 38 optimal weight: 0.0870 chunk 57 optimal weight: 2.9990 overall best weight: 0.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8269 Z= 0.171 Angle : 0.510 9.964 11193 Z= 0.263 Chirality : 0.040 0.150 1221 Planarity : 0.003 0.038 1466 Dihedral : 5.862 51.262 1133 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.97 % Allowed : 14.87 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.27), residues: 1007 helix: 1.67 (0.23), residues: 547 sheet: -0.88 (0.52), residues: 86 loop : 0.23 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 569 HIS 0.004 0.001 HIS D 732 PHE 0.011 0.001 PHE D 879 TYR 0.008 0.001 TYR D 853 ARG 0.002 0.000 ARG A 893 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 0.951 Fit side-chains outliers start: 17 outliers final: 11 residues processed: 63 average time/residue: 1.1087 time to fit residues: 75.9135 Evaluate side-chains 59 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 569 TRP Chi-restraints excluded: chain D residue 609 ASN Chi-restraints excluded: chain D residue 705 MET Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 849 ILE Chi-restraints excluded: chain D residue 967 ILE Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 609 ASN Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 967 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.2980 chunk 18 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 92 optimal weight: 0.0970 chunk 84 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8269 Z= 0.274 Angle : 0.569 10.276 11193 Z= 0.297 Chirality : 0.043 0.150 1221 Planarity : 0.004 0.038 1466 Dihedral : 6.252 50.834 1133 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.86 % Allowed : 15.45 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.27), residues: 1007 helix: 1.59 (0.22), residues: 545 sheet: -0.95 (0.50), residues: 86 loop : 0.15 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 644 HIS 0.006 0.001 HIS A 536 PHE 0.013 0.001 PHE D 879 TYR 0.010 0.001 TYR D 685 ARG 0.003 0.000 ARG A 593 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.890 Fit side-chains REVERT: A 845 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7162 (ptm160) outliers start: 16 outliers final: 12 residues processed: 60 average time/residue: 1.1337 time to fit residues: 73.7158 Evaluate side-chains 61 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 569 TRP Chi-restraints excluded: chain D residue 609 ASN Chi-restraints excluded: chain D residue 705 MET Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 849 ILE Chi-restraints excluded: chain D residue 967 ILE Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 609 ASN Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 845 ARG Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 967 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8269 Z= 0.325 Angle : 0.613 12.128 11193 Z= 0.317 Chirality : 0.044 0.150 1221 Planarity : 0.004 0.038 1466 Dihedral : 6.396 50.855 1133 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.97 % Allowed : 15.45 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.27), residues: 1007 helix: 1.52 (0.22), residues: 545 sheet: -1.01 (0.49), residues: 86 loop : 0.07 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 644 HIS 0.006 0.001 HIS A 536 PHE 0.014 0.002 PHE D 879 TYR 0.012 0.002 TYR A 685 ARG 0.003 0.000 ARG A 593 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.978 Fit side-chains REVERT: A 845 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7203 (ptm160) outliers start: 17 outliers final: 12 residues processed: 60 average time/residue: 1.1204 time to fit residues: 72.8920 Evaluate side-chains 60 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 569 TRP Chi-restraints excluded: chain D residue 609 ASN Chi-restraints excluded: chain D residue 705 MET Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 849 ILE Chi-restraints excluded: chain D residue 967 ILE Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 609 ASN Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 845 ARG Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 967 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 91 optimal weight: 0.0570 chunk 79 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 882 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8269 Z= 0.180 Angle : 0.547 11.052 11193 Z= 0.277 Chirality : 0.041 0.151 1221 Planarity : 0.004 0.037 1466 Dihedral : 5.961 50.579 1133 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.51 % Allowed : 15.80 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.27), residues: 1007 helix: 1.66 (0.23), residues: 545 sheet: -0.94 (0.51), residues: 86 loop : 0.16 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 799 HIS 0.004 0.001 HIS D 732 PHE 0.012 0.001 PHE D 879 TYR 0.009 0.001 TYR D 853 ARG 0.002 0.000 ARG A 893 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.991 Fit side-chains outliers start: 13 outliers final: 11 residues processed: 62 average time/residue: 1.1175 time to fit residues: 75.2938 Evaluate side-chains 60 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 569 TRP Chi-restraints excluded: chain D residue 609 ASN Chi-restraints excluded: chain D residue 705 MET Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain D residue 849 ILE Chi-restraints excluded: chain D residue 967 ILE Chi-restraints excluded: chain A residue 569 TRP Chi-restraints excluded: chain A residue 609 ASN Chi-restraints excluded: chain A residue 705 MET Chi-restraints excluded: chain A residue 967 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.062481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.053482 restraints weight = 20421.799| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.32 r_work: 0.2971 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8269 Z= 0.190 Angle : 0.562 12.269 11193 Z= 0.282 Chirality : 0.041 0.151 1221 Planarity : 0.004 0.038 1466 Dihedral : 5.942 50.386 1133 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.51 % Allowed : 15.91 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.27), residues: 1007 helix: 1.70 (0.23), residues: 544 sheet: -0.91 (0.51), residues: 86 loop : 0.17 (0.34), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 799 HIS 0.004 0.001 HIS D 732 PHE 0.012 0.001 PHE D 879 TYR 0.010 0.001 TYR D 853 ARG 0.002 0.000 ARG A 893 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2374.82 seconds wall clock time: 43 minutes 53.43 seconds (2633.43 seconds total)