Starting phenix.real_space_refine on Wed Mar 12 23:28:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zz6_15036/03_2025/7zz6_15036.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zz6_15036/03_2025/7zz6_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_15036/03_2025/7zz6_15036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zz6_15036/03_2025/7zz6_15036.map" model { file = "/net/cci-nas-00/data/ceres_data/7zz6_15036/03_2025/7zz6_15036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zz6_15036/03_2025/7zz6_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-5624/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: 5.70, per 1000 atoms: 0.69 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: 2.35 Conformation dependent library (CDL) restraints added in 938.0 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: 0.97 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: 2.40 Time building geometry restraints manager: 2.72 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: 2.500 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.860 Find NCS groups from input model: 0.320 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:14.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.250 ------------------------------------------------------------------------------- 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 : 1.011 Fit side-chains outliers start: 30 outliers final: 26 residues processed: 75 average time/residue: 1.0127 time to fit residues: 82.7782 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 : 0.939 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.062110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.053292 restraints weight = 20519.424| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.30 r_work: 0.2959 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 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 : 1.047 Fit side-chains REVERT: D 929 ASP cc_start: 0.7873 (p0) cc_final: 0.7667 (p0) outliers start: 26 outliers final: 10 residues processed: 71 average time/residue: 1.2368 time to fit residues: 94.5381 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 : 0.899 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 69 optimal weight: 0.0970 chunk 22 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 = 0.3348 r_free = 0.3348 target = 0.062218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.053213 restraints weight = 20617.747| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.32 r_work: 0.2958 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8269 Z= 0.189 Angle : 0.504 5.459 11193 Z= 0.268 Chirality : 0.041 0.152 1221 Planarity : 0.004 0.037 1466 Dihedral : 6.252 52.206 1136 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.90 % Allowed : 14.52 % 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: 1.09 (0.27), residues: 1007 helix: 1.44 (0.22), residues: 546 sheet: -0.88 (0.50), residues: 86 loop : 0.21 (0.34), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 799 HIS 0.005 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 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: 25 poor density : 48 time to evaluate : 0.927 Fit side-chains REVERT: A 845 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7796 (ptm160) REVERT: A 893 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7790 (ttt90) outliers start: 25 outliers final: 14 residues processed: 67 average time/residue: 1.1315 time to fit residues: 82.0648 Evaluate side-chains 61 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 45 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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 745 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 93 optimal weight: 0.7980 chunk 35 optimal weight: 0.0980 chunk 82 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 58 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.062933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.054019 restraints weight = 20621.333| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.31 r_work: 0.2984 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8269 Z= 0.165 Angle : 0.488 7.988 11193 Z= 0.257 Chirality : 0.040 0.149 1221 Planarity : 0.003 0.037 1466 Dihedral : 6.053 52.433 1136 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.14 % Allowed : 13.94 % Favored : 82.93 % 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: 1.20 (0.27), residues: 1007 helix: 1.55 (0.23), residues: 546 sheet: -0.86 (0.51), residues: 86 loop : 0.22 (0.35), residues: 375 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 0.007 0.001 TYR D 518 ARG 0.001 0.000 ARG D 845 *********************** 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 78 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 51 time to evaluate : 1.002 Fit side-chains REVERT: D 929 ASP cc_start: 0.7726 (p0) cc_final: 0.7440 (p0) REVERT: A 845 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7720 (ptm160) REVERT: A 893 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7759 (ttt90) outliers start: 27 outliers final: 12 residues processed: 73 average time/residue: 1.0879 time to fit residues: 86.1017 Evaluate side-chains 60 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 893 ARG 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 51 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 = 0.3328 r_free = 0.3328 target = 0.061420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.052363 restraints weight = 20179.529| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.29 r_work: 0.2936 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8269 Z= 0.265 Angle : 0.563 8.811 11193 Z= 0.292 Chirality : 0.043 0.164 1221 Planarity : 0.004 0.038 1466 Dihedral : 6.343 51.515 1135 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.56 % Allowed : 14.17 % Favored : 83.28 % 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: 1.13 (0.27), residues: 1007 helix: 1.51 (0.22), residues: 545 sheet: -0.94 (0.51), residues: 86 loop : 0.19 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 799 HIS 0.006 0.001 HIS A 536 PHE 0.014 0.001 PHE D 879 TYR 0.010 0.001 TYR D 685 ARG 0.003 0.000 ARG A 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 69 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 47 time to evaluate : 0.989 Fit side-chains REVERT: A 845 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7792 (ptm160) outliers start: 22 outliers final: 13 residues processed: 64 average time/residue: 1.1480 time to fit residues: 79.4643 Evaluate side-chains 60 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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 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 52 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 28 optimal weight: 0.0770 chunk 27 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 = 0.3355 r_free = 0.3355 target = 0.062445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.053473 restraints weight = 20543.888| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.32 r_work: 0.2970 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.1274 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= 0.183 Angle : 0.518 9.458 11193 Z= 0.267 Chirality : 0.041 0.150 1221 Planarity : 0.004 0.038 1466 Dihedral : 6.078 51.586 1135 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.16 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: 1.22 (0.27), residues: 1007 helix: 1.60 (0.23), residues: 545 sheet: -0.90 (0.51), residues: 86 loop : 0.19 (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 0.007 0.001 TYR A 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 67 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 0.962 Fit side-chains outliers start: 17 outliers final: 12 residues processed: 63 average time/residue: 1.0587 time to fit residues: 72.5380 Evaluate side-chains 59 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 37 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3347 r_free = 0.3347 target = 0.062066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.053182 restraints weight = 20492.283| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.30 r_work: 0.2963 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8269 Z= 0.202 Angle : 0.541 10.171 11193 Z= 0.276 Chirality : 0.041 0.150 1221 Planarity : 0.004 0.038 1466 Dihedral : 6.018 51.275 1133 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.56 % Allowed : 14.52 % Favored : 82.93 % 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: 1.24 (0.27), residues: 1007 helix: 1.62 (0.22), residues: 545 sheet: -0.90 (0.51), residues: 86 loop : 0.21 (0.34), residues: 376 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 0.009 0.001 TYR D 853 ARG 0.002 0.000 ARG A 593 *********************** 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 70 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 48 time to evaluate : 1.058 Fit side-chains outliers start: 22 outliers final: 13 residues processed: 63 average time/residue: 1.0484 time to fit residues: 72.1043 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 : 0.906 ------------------------------------------------------------------------------- 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 849 ILE Chi-restraints excluded: chain A residue 856 VAL 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 43 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 0.0020 chunk 60 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- 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 = 0.3361 r_free = 0.3361 target = 0.062690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.053688 restraints weight = 20662.312| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.32 r_work: 0.2977 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.1365 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= 0.180 Angle : 0.521 10.298 11193 Z= 0.267 Chirality : 0.041 0.149 1221 Planarity : 0.003 0.038 1466 Dihedral : 5.897 51.134 1133 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.86 % Allowed : 15.56 % 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: 1.27 (0.27), residues: 1007 helix: 1.67 (0.23), residues: 545 sheet: -0.88 (0.51), residues: 86 loop : 0.18 (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 0.007 0.001 TYR D 685 ARG 0.002 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 67 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.870 Fit side-chains outliers start: 16 outliers final: 10 residues processed: 63 average time/residue: 1.0758 time to fit residues: 73.7950 Evaluate side-chains 57 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 705 MET 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 87 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 3 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 = 0.3316 r_free = 0.3316 target = 0.060947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.051779 restraints weight = 20768.760| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.33 r_work: 0.2916 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9004 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8269 Z= 0.332 Angle : 0.610 10.859 11193 Z= 0.317 Chirality : 0.044 0.149 1221 Planarity : 0.004 0.038 1466 Dihedral : 6.258 50.998 1131 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.74 % Allowed : 15.45 % 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: 1.07 (0.27), residues: 1007 helix: 1.49 (0.22), residues: 545 sheet: -0.97 (0.50), residues: 86 loop : 0.10 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 644 HIS 0.006 0.001 HIS A 536 PHE 0.013 0.002 PHE D 879 TYR 0.012 0.002 TYR A 853 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 62 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.906 Fit side-chains REVERT: D 614 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7692 (pm20) outliers start: 15 outliers final: 10 residues processed: 57 average time/residue: 1.1147 time to fit residues: 68.9372 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 : 0.982 ------------------------------------------------------------------------------- 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 614 GLN 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 705 MET 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 18 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.061076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.051948 restraints weight = 20566.533| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.32 r_work: 0.2923 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8269 Z= 0.302 Angle : 0.606 11.544 11193 Z= 0.312 Chirality : 0.044 0.150 1221 Planarity : 0.004 0.039 1466 Dihedral : 6.209 50.690 1131 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.63 % Allowed : 15.56 % 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: 1.02 (0.27), residues: 1007 helix: 1.45 (0.22), residues: 545 sheet: -0.99 (0.50), residues: 86 loop : 0.08 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 644 HIS 0.006 0.001 HIS A 536 PHE 0.013 0.002 PHE D 879 TYR 0.011 0.001 TYR A 685 ARG 0.003 0.000 ARG A 593 ********************** 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 62 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.929 Fit side-chains REVERT: D 614 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7727 (pm20) outliers start: 14 outliers final: 11 residues processed: 59 average time/residue: 1.2051 time to fit residues: 77.0748 Evaluate side-chains 60 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 1.134 ------------------------------------------------------------------------------- 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 614 GLN 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 705 MET 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 88 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.061605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.052539 restraints weight = 20591.692| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.31 r_work: 0.2941 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8269 Z= 0.246 Angle : 0.590 12.388 11193 Z= 0.299 Chirality : 0.042 0.152 1221 Planarity : 0.004 0.040 1466 Dihedral : 6.064 50.505 1131 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.39 % Allowed : 15.80 % 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: 1.12 (0.27), residues: 1007 helix: 1.53 (0.22), residues: 545 sheet: -0.97 (0.50), residues: 86 loop : 0.14 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5907.11 seconds wall clock time: 102 minutes 7.19 seconds (6127.19 seconds total)