Starting phenix.real_space_refine on Fri Sep 11 15:38:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6w5c_21541/09_2026/6w5c_21541.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w5c_21541/09_2026/6w5c_21541.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6w5c_21541/09_2026/6w5c_21541.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6w5c_21541/09_2026/6w5c_21541.cif" model { file = "/net/cci-nas-00/data/ceres_data/6w5c_21541/09_2026/6w5c_21541.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w5c_21541/09_2026/6w5c_21541.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6w5c_21541/09_2026/6w5c_21541.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w5c_21541/09_2026/6w5c_21541.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.009 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: 5 Type Number sf(0) Gaussians P 105 5.49 5 S 36 5.16 5 C 6111 2.51 5 N 1769 2.21 5 O 2162 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10183 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 8000 Classifications: {'peptide': 1023} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 35, 'TRANS': 987} Chain breaks: 6 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 301 Unresolved non-hydrogen angles: 368 Unresolved non-hydrogen dihedrals: 246 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'ASP:plan': 8, 'ASN:plan1': 10, 'GLN:plan1': 5, 'TYR:plan': 2, 'ARG:plan': 4, 'GLU:plan': 6, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 143 Chain: "C" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 740 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "D" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 199 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "E" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 189 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "B" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1055 Classifications: {'RNAv2': 50} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 9, 'rna3p_pur': 17, 'rna3p_pyr': 21} Link IDs: {'rna2p': 12, 'rna3p': 37} Time building chain proxies: 2.36, per 1000 atoms: 0.23 Number of scatterers: 10183 At special positions: 0 Unit cell: (90.61, 134.316, 101.27, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 105 15.00 O 2162 8.00 N 1769 7.00 C 6111 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: 0.93 Conformation dependent library (CDL) restraints added in 291.9 milliseconds 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1946 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 6 sheets defined 56.4% alpha, 6.9% beta 36 base pairs and 69 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 23 through 54 Proline residue: A 42 - end of helix Processing helix chain 'A' and resid 70 through 80 removed outlier: 3.692A pdb=" N LEU A 75 " --> pdb=" O ASP A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 95 No H-bonds generated for 'chain 'A' and resid 93 through 95' Processing helix chain 'A' and resid 96 through 104 Processing helix chain 'A' and resid 110 through 118 Processing helix chain 'A' and resid 132 through 143 Processing helix chain 'A' and resid 145 through 159 Processing helix chain 'A' and resid 168 through 177 Processing helix chain 'A' and resid 184 through 198 Processing helix chain 'A' and resid 212 through 219 Processing helix chain 'A' and resid 224 through 232 Processing helix chain 'A' and resid 242 through 251 Processing helix chain 'A' and resid 261 through 269 removed outlier: 4.194A pdb=" N ASN A 265 " --> pdb=" O SER A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 281 through 293 Processing helix chain 'A' and resid 297 through 333 removed outlier: 3.520A pdb=" N SER A 310 " --> pdb=" O GLU A 306 " (cutoff:3.500A) Proline residue: A 311 - end of helix Processing helix chain 'A' and resid 337 through 346 Processing helix chain 'A' and resid 347 through 350 removed outlier: 3.792A pdb=" N SER A 350 " --> pdb=" O PHE A 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 347 through 350' Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.771A pdb=" N GLY A 369 " --> pdb=" O HIS A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 393 removed outlier: 3.668A pdb=" N SER A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 422 removed outlier: 3.798A pdb=" N LYS A 404 " --> pdb=" O GLU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 439 Processing helix chain 'A' and resid 444 through 463 Processing helix chain 'A' and resid 491 through 501 removed outlier: 3.663A pdb=" N LEU A 495 " --> pdb=" O PRO A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 540 removed outlier: 3.577A pdb=" N LEU A 537 " --> pdb=" O SER A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 581 Processing helix chain 'A' and resid 582 through 584 No H-bonds generated for 'chain 'A' and resid 582 through 584' Processing helix chain 'A' and resid 585 through 601 Processing helix chain 'A' and resid 708 through 722 removed outlier: 3.644A pdb=" N LYS A 721 " --> pdb=" O SER A 717 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR A 722 " --> pdb=" O PHE A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 771 Processing helix chain 'A' and resid 772 through 777 removed outlier: 3.527A pdb=" N ALA A 775 " --> pdb=" O SER A 772 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N LYS A 776 " --> pdb=" O SER A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 787 Processing helix chain 'A' and resid 800 through 822 removed outlier: 3.781A pdb=" N PHE A 807 " --> pdb=" O SER A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 846 Processing helix chain 'A' and resid 846 through 886 Processing helix chain 'A' and resid 905 through 914 removed outlier: 3.794A pdb=" N ASP A 914 " --> pdb=" O SER A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 929 Processing helix chain 'A' and resid 967 through 971 removed outlier: 3.557A pdb=" N LEU A 971 " --> pdb=" O PRO A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 984 removed outlier: 3.507A pdb=" N ARG A 976 " --> pdb=" O THR A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 1008 removed outlier: 4.333A pdb=" N ALA A 994 " --> pdb=" O ARG A 990 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR A 995 " --> pdb=" O PRO A 991 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A1007 " --> pdb=" O PHE A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1015 Processing helix chain 'A' and resid 1018 through 1033 Processing helix chain 'A' and resid 1072 through 1082 Processing helix chain 'A' and resid 1085 through 1090 Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 14 removed outlier: 6.997A pdb=" N ASN A 477 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N GLY A 486 " --> pdb=" O ASN A 477 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLY A 479 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ILE A 488 " --> pdb=" O GLY A 479 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N LEU A 485 " --> pdb=" O LYS A 515 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG A 523 " --> pdb=" O ASN A 518 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ALA A 530 " --> pdb=" O ILE A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 81 through 84 removed outlier: 3.586A pdb=" N LYS A 81 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 678 through 683 removed outlier: 6.270A pdb=" N GLU A 660 " --> pdb=" O PRO A 678 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU A 680 " --> pdb=" O ALA A 658 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU A 894 " --> pdb=" O TYR A 646 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL A 937 " --> pdb=" O VAL A 889 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE A 891 " --> pdb=" O VAL A 937 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL A 939 " --> pdb=" O ILE A 891 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLY A 893 " --> pdb=" O VAL A 939 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 669 through 670 Processing sheet with id=AA5, first strand: chain 'A' and resid 687 through 688 removed outlier: 3.541A pdb=" N TYR A 695 " --> pdb=" O SER A 688 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1049 through 1050 removed outlier: 3.604A pdb=" N THR A1059 " --> pdb=" O VAL A1070 " (cutoff:3.500A) 425 hydrogen bonds defined for protein. 1251 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 92 hydrogen bonds 184 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 69 stacking parallelities Total time for adding SS restraints: 2.89 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2562 1.33 - 1.45: 2443 1.45 - 1.57: 5330 1.57 - 1.69: 206 1.69 - 1.81: 60 Bond restraints: 10601 Sorted by residual: bond pdb=" N TYR A 754 " pdb=" CA TYR A 754 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.33e-02 5.65e+03 1.11e+01 bond pdb=" N ASP A 788 " pdb=" CA ASP A 788 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.24e-02 6.50e+03 1.09e+01 bond pdb=" C3' DC C 34 " pdb=" C2' DC C 34 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.08e+00 bond pdb=" C3' DA C 4 " pdb=" C2' DA C 4 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.00e+00 bond pdb=" C3' DG D 3 " pdb=" C2' DG D 3 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.73e+00 ... (remaining 10596 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 14173 1.73 - 3.46: 495 3.46 - 5.18: 87 5.18 - 6.91: 12 6.91 - 8.64: 7 Bond angle restraints: 14774 Sorted by residual: angle pdb=" N PRO A 987 " pdb=" CA PRO A 987 " pdb=" CB PRO A 987 " ideal model delta sigma weight residual 103.36 110.43 -7.07 8.80e-01 1.29e+00 6.45e+01 angle pdb=" N PRO A 955 " pdb=" CA PRO A 955 " pdb=" CB PRO A 955 " ideal model delta sigma weight residual 103.25 110.33 -7.08 1.05e+00 9.07e-01 4.55e+01 angle pdb=" N ASN A1064 " pdb=" CA ASN A1064 " pdb=" C ASN A1064 " ideal model delta sigma weight residual 111.07 105.24 5.83 1.07e+00 8.73e-01 2.97e+01 angle pdb=" C VAL A1061 " pdb=" N ASN A1062 " pdb=" CA ASN A1062 " ideal model delta sigma weight residual 122.77 129.88 -7.11 1.33e+00 5.65e-01 2.86e+01 angle pdb=" N ASP A 788 " pdb=" CA ASP A 788 " pdb=" C ASP A 788 " ideal model delta sigma weight residual 111.40 117.85 -6.45 1.22e+00 6.72e-01 2.79e+01 ... (remaining 14769 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.25: 5789 30.25 - 60.50: 349 60.50 - 90.74: 29 90.74 - 120.99: 0 120.99 - 151.24: 1 Dihedral angle restraints: 6168 sinusoidal: 3159 harmonic: 3009 Sorted by residual: dihedral pdb=" C4' G B 1 " pdb=" C3' G B 1 " pdb=" C2' G B 1 " pdb=" C1' G B 1 " ideal model delta sinusoidal sigma weight residual 36.35 -38.25 74.59 1 3.10e+00 1.04e-01 7.34e+02 dihedral pdb=" C4' C B -8 " pdb=" C3' C B -8 " pdb=" C2' C B -8 " pdb=" C1' C B -8 " ideal model delta sinusoidal sigma weight residual 36.34 -36.23 72.58 1 3.10e+00 1.04e-01 7.00e+02 dihedral pdb=" C4' U B -9 " pdb=" C3' U B -9 " pdb=" C2' U B -9 " pdb=" C1' U B -9 " ideal model delta sinusoidal sigma weight residual 36.34 -36.11 72.45 1 3.10e+00 1.04e-01 6.98e+02 ... (remaining 6165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1358 0.059 - 0.118: 180 0.118 - 0.177: 58 0.177 - 0.236: 60 0.236 - 0.295: 21 Chirality restraints: 1677 Sorted by residual: chirality pdb=" C2' U B -17 " pdb=" C3' U B -17 " pdb=" O2' U B -17 " pdb=" C1' U B -17 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C2' G B 1 " pdb=" C3' G B 1 " pdb=" O2' G B 1 " pdb=" C1' G B 1 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C2' U B -5 " pdb=" C3' U B -5 " pdb=" O2' U B -5 " pdb=" C1' U B -5 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 1674 not shown) Planarity restraints: 1508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 693 " 0.019 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C LYS A 693 " -0.067 2.00e-02 2.50e+03 pdb=" O LYS A 693 " 0.026 2.00e-02 2.50e+03 pdb=" N SER A 694 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 754 " -0.042 2.00e-02 2.50e+03 2.33e-02 1.09e+01 pdb=" CG TYR A 754 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR A 754 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR A 754 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR A 754 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR A 754 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 754 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 754 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 787 " 0.017 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C ARG A 787 " -0.057 2.00e-02 2.50e+03 pdb=" O ARG A 787 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP A 788 " 0.019 2.00e-02 2.50e+03 ... (remaining 1505 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 297 2.66 - 3.22: 9836 3.22 - 3.78: 17541 3.78 - 4.34: 24337 4.34 - 4.90: 37584 Nonbonded interactions: 89595 Sorted by model distance: nonbonded pdb=" OE1 GLN A 186 " pdb=" OG1 THR A 187 " model vdw 2.103 3.040 nonbonded pdb=" O TYR A 104 " pdb=" OG SER A 105 " model vdw 2.134 3.040 nonbonded pdb=" OH TYR A 542 " pdb=" OE1 GLU A 596 " model vdw 2.202 3.040 nonbonded pdb=" OD2 ASP A 647 " pdb=" ND2 ASN A 649 " model vdw 2.206 3.120 nonbonded pdb=" NE ARG A 715 " pdb=" OE2 GLU A 781 " model vdw 2.215 3.120 ... (remaining 89590 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.180 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.270 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10601 Z= 0.314 Angle : 0.760 8.640 14774 Z= 0.497 Chirality : 0.067 0.295 1677 Planarity : 0.003 0.039 1508 Dihedral : 17.352 151.239 4222 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.43 % Favored : 92.37 % Rotamer: Outliers : 0.85 % Allowed : 4.00 % Favored : 95.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.26), residues: 1009 helix: 0.66 (0.23), residues: 550 sheet: -2.34 (0.52), residues: 99 loop : -3.16 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 652 TYR 0.042 0.002 TYR A 754 PHE 0.009 0.001 PHE A 536 TRP 0.017 0.002 TRP A 79 HIS 0.003 0.001 HIS A 711 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.31 (10601) covalent geometry : angle 0.75951 / 0.50 (14774) hydrogen bonds : bond 0.15168 / 10.33 ( 517) hydrogen bonds : angle 6.81617 / 4.85 ( 1435) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: A 186 GLN cc_start: 0.7013 (OUTLIER) cc_final: 0.6528 (pm20) REVERT: A 273 PHE cc_start: 0.7363 (m-80) cc_final: 0.7096 (m-80) REVERT: A 450 ASP cc_start: 0.7524 (m-30) cc_final: 0.7151 (m-30) REVERT: A 740 MET cc_start: 0.6482 (mtp) cc_final: 0.6161 (mtm) REVERT: A 873 ASN cc_start: 0.8281 (OUTLIER) cc_final: 0.8061 (t0) REVERT: A 1001 MET cc_start: 0.7892 (mmt) cc_final: 0.7571 (mmm) outliers start: 7 outliers final: 2 residues processed: 107 average time/residue: 0.5462 time to fit residues: 62.8985 Evaluate side-chains 71 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 186 GLN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 873 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 8.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 459 HIS A 497 HIS A 654 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.123672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.089987 restraints weight = 16474.307| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.17 r_work: 0.3186 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10601 Z= 0.252 Angle : 1.092 26.550 14774 Z= 0.482 Chirality : 0.100 1.179 1677 Planarity : 0.005 0.078 1508 Dihedral : 18.305 150.863 2320 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.83 % Favored : 92.07 % Rotamer: Outliers : 2.42 % Allowed : 10.30 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.26), residues: 1009 helix: 0.76 (0.22), residues: 554 sheet: -2.28 (0.50), residues: 99 loop : -2.91 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 652 TYR 0.017 0.002 TYR A 754 PHE 0.011 0.002 PHE A 718 TRP 0.019 0.003 TRP A 79 HIS 0.005 0.001 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.25 (10601) covalent geometry : angle 1.09238 / 0.48 (14774) hydrogen bonds : bond 0.04691 / 3.13 ( 517) hydrogen bonds : angle 4.64420 / 3.39 ( 1435) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 273 PHE cc_start: 0.7343 (m-80) cc_final: 0.7034 (m-80) REVERT: A 345 GLU cc_start: 0.8456 (tt0) cc_final: 0.8102 (mm-30) REVERT: A 450 ASP cc_start: 0.7914 (m-30) cc_final: 0.7579 (m-30) REVERT: A 740 MET cc_start: 0.6561 (mtp) cc_final: 0.6332 (mtm) outliers start: 20 outliers final: 6 residues processed: 89 average time/residue: 0.5691 time to fit residues: 54.8633 Evaluate side-chains 71 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 694 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 88 optimal weight: 0.6980 chunk 102 optimal weight: 50.0000 chunk 26 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 94 optimal weight: 40.0000 chunk 99 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 71 optimal weight: 9.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 GLN A 873 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.124544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.091194 restraints weight = 16454.771| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.20 r_work: 0.3184 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10601 Z= 0.201 Angle : 0.824 13.691 14774 Z= 0.389 Chirality : 0.067 0.805 1677 Planarity : 0.004 0.072 1508 Dihedral : 18.521 147.431 2314 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 1.94 % Allowed : 10.30 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.27), residues: 1009 helix: 1.04 (0.22), residues: 549 sheet: -1.92 (0.50), residues: 99 loop : -2.77 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 26 TYR 0.023 0.002 TYR A 275 PHE 0.012 0.002 PHE A1090 TRP 0.019 0.002 TRP A 377 HIS 0.005 0.001 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.20 (10601) covalent geometry : angle 0.82437 / 0.39 (14774) hydrogen bonds : bond 0.04302 / 2.74 ( 517) hydrogen bonds : angle 4.29200 / 3.14 ( 1435) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 345 GLU cc_start: 0.8495 (tt0) cc_final: 0.8143 (mm-30) REVERT: A 450 ASP cc_start: 0.7918 (m-30) cc_final: 0.7601 (m-30) REVERT: A 526 LYS cc_start: 0.8561 (mttt) cc_final: 0.8308 (mttt) REVERT: A 1046 MET cc_start: 0.7852 (ptp) cc_final: 0.7589 (mtm) REVERT: A 1088 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8169 (mttt) outliers start: 16 outliers final: 7 residues processed: 87 average time/residue: 0.4781 time to fit residues: 45.5712 Evaluate side-chains 75 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 654 ASN Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1074 ASP Chi-restraints excluded: chain A residue 1088 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 106 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 101 optimal weight: 0.3980 chunk 104 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 654 ASN A 873 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.124114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.090618 restraints weight = 16582.952| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.21 r_work: 0.3173 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10601 Z= 0.208 Angle : 0.801 13.304 14774 Z= 0.380 Chirality : 0.063 0.709 1677 Planarity : 0.004 0.074 1508 Dihedral : 18.504 149.397 2314 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 2.67 % Allowed : 11.15 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.27), residues: 1009 helix: 1.13 (0.22), residues: 549 sheet: -1.76 (0.51), residues: 99 loop : -2.69 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 22 TYR 0.011 0.002 TYR A 996 PHE 0.022 0.002 PHE A 191 TRP 0.023 0.002 TRP A 377 HIS 0.004 0.001 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.21 (10601) covalent geometry : angle 0.80058 / 0.38 (14774) hydrogen bonds : bond 0.03943 / 2.56 ( 517) hydrogen bonds : angle 4.16021 / 3.04 ( 1435) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 273 PHE cc_start: 0.7534 (m-80) cc_final: 0.7203 (m-80) REVERT: A 345 GLU cc_start: 0.8489 (tt0) cc_final: 0.8209 (mm-30) REVERT: A 389 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7639 (mt-10) REVERT: A 412 GLN cc_start: 0.8041 (tm-30) cc_final: 0.7780 (tm-30) REVERT: A 446 ASP cc_start: 0.7913 (p0) cc_final: 0.7681 (p0) REVERT: A 450 ASP cc_start: 0.7950 (m-30) cc_final: 0.7634 (m-30) REVERT: A 526 LYS cc_start: 0.8549 (mttt) cc_final: 0.8319 (mttt) REVERT: A 531 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8549 (mt) REVERT: A 870 VAL cc_start: 0.9069 (OUTLIER) cc_final: 0.8769 (m) REVERT: A 913 MET cc_start: 0.8866 (mtm) cc_final: 0.8407 (mtm) REVERT: A 1046 MET cc_start: 0.7830 (ptp) cc_final: 0.7586 (mtm) REVERT: A 1088 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8153 (mttt) outliers start: 22 outliers final: 11 residues processed: 93 average time/residue: 0.4847 time to fit residues: 49.3110 Evaluate side-chains 87 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 928 VAL Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1074 ASP Chi-restraints excluded: chain A residue 1088 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 80 optimal weight: 4.9990 chunk 70 optimal weight: 0.0040 chunk 90 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 20 optimal weight: 50.0000 chunk 26 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 102 optimal weight: 50.0000 chunk 30 optimal weight: 7.9990 overall best weight: 2.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 GLN A 654 ASN A1067 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.124045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.090370 restraints weight = 16550.551| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.21 r_work: 0.3172 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10601 Z= 0.215 Angle : 0.774 12.251 14774 Z= 0.370 Chirality : 0.061 0.708 1677 Planarity : 0.004 0.045 1508 Dihedral : 18.438 146.555 2314 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 2.30 % Allowed : 12.24 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.27), residues: 1009 helix: 1.16 (0.22), residues: 550 sheet: -1.58 (0.52), residues: 99 loop : -2.74 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 523 TYR 0.011 0.002 TYR A 700 PHE 0.029 0.002 PHE A 191 TRP 0.027 0.002 TRP A 377 HIS 0.005 0.001 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.22 (10601) covalent geometry : angle 0.77368 / 0.37 (14774) hydrogen bonds : bond 0.03929 / 2.56 ( 517) hydrogen bonds : angle 4.10658 / 3.01 ( 1435) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 273 PHE cc_start: 0.7539 (m-80) cc_final: 0.7232 (m-80) REVERT: A 345 GLU cc_start: 0.8475 (tt0) cc_final: 0.8267 (mm-30) REVERT: A 389 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7613 (mt-10) REVERT: A 446 ASP cc_start: 0.7927 (p0) cc_final: 0.7711 (p0) REVERT: A 450 ASP cc_start: 0.7980 (m-30) cc_final: 0.7669 (m-30) REVERT: A 531 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8563 (mt) REVERT: A 776 LYS cc_start: 0.8834 (tmtt) cc_final: 0.8522 (tptp) REVERT: A 870 VAL cc_start: 0.9082 (OUTLIER) cc_final: 0.8772 (m) REVERT: A 1046 MET cc_start: 0.7831 (ptp) cc_final: 0.7595 (mtm) REVERT: A 1088 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8172 (mttt) outliers start: 19 outliers final: 10 residues processed: 95 average time/residue: 0.5078 time to fit residues: 52.5031 Evaluate side-chains 85 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1063 TRP Chi-restraints excluded: chain A residue 1074 ASP Chi-restraints excluded: chain A residue 1088 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 23 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 78 optimal weight: 0.8980 chunk 94 optimal weight: 30.0000 chunk 73 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 GLN A 190 GLN A 654 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.126609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.093250 restraints weight = 16634.810| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.23 r_work: 0.3213 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10601 Z= 0.150 Angle : 0.721 11.466 14774 Z= 0.347 Chirality : 0.055 0.607 1677 Planarity : 0.004 0.038 1508 Dihedral : 18.352 148.438 2314 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 1.45 % Allowed : 13.45 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.27), residues: 1009 helix: 1.29 (0.22), residues: 549 sheet: -1.42 (0.52), residues: 99 loop : -2.67 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1033 TYR 0.010 0.001 TYR A 646 PHE 0.028 0.001 PHE A 191 TRP 0.021 0.002 TRP A 377 HIS 0.005 0.001 HIS A 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 (10601) covalent geometry : angle 0.72149 / 0.35 (14774) hydrogen bonds : bond 0.03688 / 2.38 ( 517) hydrogen bonds : angle 3.95536 / 2.90 ( 1435) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 273 PHE cc_start: 0.7637 (m-80) cc_final: 0.7391 (m-80) REVERT: A 345 GLU cc_start: 0.8437 (tt0) cc_final: 0.8197 (mm-30) REVERT: A 386 LYS cc_start: 0.8309 (mtpp) cc_final: 0.8040 (mtmm) REVERT: A 446 ASP cc_start: 0.7896 (p0) cc_final: 0.7695 (p0) REVERT: A 450 ASP cc_start: 0.7978 (m-30) cc_final: 0.7667 (m-30) REVERT: A 531 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8463 (mt) REVERT: A 776 LYS cc_start: 0.8869 (tmtt) cc_final: 0.8524 (tptp) REVERT: A 821 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8579 (tt) REVERT: A 870 VAL cc_start: 0.9011 (OUTLIER) cc_final: 0.8752 (m) REVERT: A 913 MET cc_start: 0.8852 (mtm) cc_final: 0.8327 (mtm) REVERT: A 973 GLU cc_start: 0.8549 (tt0) cc_final: 0.8067 (mm-30) outliers start: 12 outliers final: 5 residues processed: 87 average time/residue: 0.5227 time to fit residues: 49.3150 Evaluate side-chains 84 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 1074 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 18 optimal weight: 20.0000 chunk 78 optimal weight: 2.9990 chunk 8 optimal weight: 0.0010 chunk 16 optimal weight: 8.9990 chunk 84 optimal weight: 0.5980 chunk 54 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 10 optimal weight: 0.0370 chunk 86 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 overall best weight: 1.9268 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 654 ASN A1062 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.125948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.092655 restraints weight = 16478.780| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.21 r_work: 0.3198 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10601 Z= 0.172 Angle : 0.723 11.223 14774 Z= 0.348 Chirality : 0.055 0.573 1677 Planarity : 0.004 0.036 1508 Dihedral : 18.299 148.998 2313 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 2.06 % Allowed : 13.82 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.27), residues: 1009 helix: 1.30 (0.22), residues: 550 sheet: -1.28 (0.53), residues: 99 loop : -2.65 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 523 TYR 0.012 0.001 TYR A 996 PHE 0.027 0.002 PHE A 191 TRP 0.026 0.002 TRP A 377 HIS 0.004 0.001 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 (10601) covalent geometry : angle 0.72316 / 0.35 (14774) hydrogen bonds : bond 0.03703 / 2.39 ( 517) hydrogen bonds : angle 3.91058 / 2.87 ( 1435) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 273 PHE cc_start: 0.7707 (m-80) cc_final: 0.7468 (m-80) REVERT: A 345 GLU cc_start: 0.8430 (tt0) cc_final: 0.8196 (mm-30) REVERT: A 412 GLN cc_start: 0.7992 (tm-30) cc_final: 0.7645 (tm-30) REVERT: A 446 ASP cc_start: 0.7928 (p0) cc_final: 0.7727 (p0) REVERT: A 450 ASP cc_start: 0.7999 (m-30) cc_final: 0.7686 (m-30) REVERT: A 821 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8610 (tt) REVERT: A 870 VAL cc_start: 0.9031 (OUTLIER) cc_final: 0.8740 (m) REVERT: A 913 MET cc_start: 0.8836 (mtm) cc_final: 0.8326 (mtm) REVERT: A 973 GLU cc_start: 0.8552 (tt0) cc_final: 0.8079 (mm-30) REVERT: A 1059 THR cc_start: 0.8447 (OUTLIER) cc_final: 0.7825 (p) outliers start: 17 outliers final: 12 residues processed: 94 average time/residue: 0.5455 time to fit residues: 55.6355 Evaluate side-chains 93 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 928 VAL Chi-restraints excluded: chain A residue 1046 MET Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1063 TRP Chi-restraints excluded: chain A residue 1074 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 65 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 GLN A 649 ASN A 654 ASN A1067 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.123199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.089315 restraints weight = 16554.504| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.21 r_work: 0.3150 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 10601 Z= 0.282 Angle : 0.811 16.294 14774 Z= 0.386 Chirality : 0.061 0.641 1677 Planarity : 0.004 0.039 1508 Dihedral : 18.401 149.171 2313 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 2.67 % Allowed : 13.33 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.27), residues: 1009 helix: 1.12 (0.22), residues: 551 sheet: -1.40 (0.53), residues: 99 loop : -2.68 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 523 TYR 0.018 0.002 TYR A 700 PHE 0.027 0.002 PHE A 191 TRP 0.032 0.003 TRP A 377 HIS 0.006 0.001 HIS A 711 Details of bonding type rmsd/Z covalent geometry : bond 0.00634 / 0.28 (10601) covalent geometry : angle 0.81109 / 0.39 (14774) hydrogen bonds : bond 0.04024 / 2.62 ( 517) hydrogen bonds : angle 4.05150 / 2.96 ( 1435) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 273 PHE cc_start: 0.7673 (m-80) cc_final: 0.7395 (m-80) REVERT: A 345 GLU cc_start: 0.8498 (tt0) cc_final: 0.8238 (mm-30) REVERT: A 389 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7644 (mt-10) REVERT: A 446 ASP cc_start: 0.7949 (p0) cc_final: 0.7719 (p0) REVERT: A 450 ASP cc_start: 0.8010 (m-30) cc_final: 0.7662 (m-30) REVERT: A 526 LYS cc_start: 0.8483 (mttt) cc_final: 0.8188 (mttt) REVERT: A 821 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8591 (tt) REVERT: A 870 VAL cc_start: 0.9109 (OUTLIER) cc_final: 0.8760 (m) outliers start: 22 outliers final: 15 residues processed: 92 average time/residue: 0.5323 time to fit residues: 53.1216 Evaluate side-chains 92 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 79 TRP Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 520 LYS Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 928 VAL Chi-restraints excluded: chain A residue 1046 MET Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1063 TRP Chi-restraints excluded: chain A residue 1074 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 88 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 GLN A 649 ASN A 654 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.125170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.091463 restraints weight = 16481.102| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.22 r_work: 0.3188 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10601 Z= 0.183 Angle : 0.744 13.900 14774 Z= 0.357 Chirality : 0.057 0.607 1677 Planarity : 0.004 0.034 1508 Dihedral : 18.363 149.574 2313 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 1.94 % Allowed : 14.42 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.27), residues: 1009 helix: 1.22 (0.22), residues: 551 sheet: -1.30 (0.54), residues: 99 loop : -2.65 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 26 TYR 0.017 0.001 TYR A 700 PHE 0.027 0.002 PHE A 191 TRP 0.031 0.002 TRP A 377 HIS 0.004 0.001 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 (10601) covalent geometry : angle 0.74440 / 0.36 (14774) hydrogen bonds : bond 0.03727 / 2.43 ( 517) hydrogen bonds : angle 3.94752 / 2.89 ( 1435) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 273 PHE cc_start: 0.7640 (m-80) cc_final: 0.7366 (m-80) REVERT: A 345 GLU cc_start: 0.8450 (tt0) cc_final: 0.8204 (mm-30) REVERT: A 386 LYS cc_start: 0.8135 (ttmm) cc_final: 0.7859 (ttpp) REVERT: A 446 ASP cc_start: 0.7957 (p0) cc_final: 0.7717 (p0) REVERT: A 450 ASP cc_start: 0.7993 (m-30) cc_final: 0.7637 (m-30) REVERT: A 821 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8562 (tt) REVERT: A 870 VAL cc_start: 0.9049 (OUTLIER) cc_final: 0.8748 (m) REVERT: A 913 MET cc_start: 0.8844 (mtm) cc_final: 0.8336 (mtm) REVERT: A 973 GLU cc_start: 0.8533 (tt0) cc_final: 0.8042 (mm-30) REVERT: A 1059 THR cc_start: 0.8433 (OUTLIER) cc_final: 0.7824 (p) outliers start: 16 outliers final: 11 residues processed: 91 average time/residue: 0.5068 time to fit residues: 50.1136 Evaluate side-chains 89 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 928 VAL Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1063 TRP Chi-restraints excluded: chain A residue 1074 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 22 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 73 optimal weight: 0.6980 chunk 19 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 110 optimal weight: 20.0000 chunk 56 optimal weight: 0.1980 chunk 34 optimal weight: 0.2980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 654 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.127402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.094306 restraints weight = 16388.935| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.21 r_work: 0.3232 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10601 Z= 0.150 Angle : 0.710 14.533 14774 Z= 0.343 Chirality : 0.053 0.510 1677 Planarity : 0.004 0.033 1508 Dihedral : 18.248 151.909 2313 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 2.06 % Allowed : 14.55 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.27), residues: 1009 helix: 1.35 (0.22), residues: 553 sheet: -1.14 (0.54), residues: 99 loop : -2.58 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 26 TYR 0.013 0.001 TYR A 700 PHE 0.023 0.002 PHE A 191 TRP 0.033 0.002 TRP A 377 HIS 0.004 0.001 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 (10601) covalent geometry : angle 0.71023 / 0.34 (14774) hydrogen bonds : bond 0.03631 / 2.34 ( 517) hydrogen bonds : angle 3.80397 / 2.79 ( 1435) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 273 PHE cc_start: 0.7844 (m-80) cc_final: 0.7632 (m-80) REVERT: A 386 LYS cc_start: 0.8252 (ttmm) cc_final: 0.7873 (mtmm) REVERT: A 412 GLN cc_start: 0.8012 (tm-30) cc_final: 0.7621 (tm-30) REVERT: A 446 ASP cc_start: 0.7873 (p0) cc_final: 0.7637 (p0) REVERT: A 450 ASP cc_start: 0.7988 (m-30) cc_final: 0.7637 (m-30) REVERT: A 526 LYS cc_start: 0.8559 (mttt) cc_final: 0.8304 (mttt) REVERT: A 870 VAL cc_start: 0.8996 (OUTLIER) cc_final: 0.8739 (m) REVERT: A 913 MET cc_start: 0.8812 (mtm) cc_final: 0.8238 (mtm) REVERT: A 973 GLU cc_start: 0.8509 (tt0) cc_final: 0.8079 (mm-30) REVERT: A 1059 THR cc_start: 0.8425 (OUTLIER) cc_final: 0.7943 (p) outliers start: 17 outliers final: 10 residues processed: 98 average time/residue: 0.5115 time to fit residues: 54.6109 Evaluate side-chains 89 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 928 VAL Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1063 TRP Chi-restraints excluded: chain A residue 1074 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 103 optimal weight: 20.0000 chunk 74 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 14 optimal weight: 8.9990 chunk 94 optimal weight: 50.0000 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 GLN A 654 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.126706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.093108 restraints weight = 16486.832| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.22 r_work: 0.3211 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10601 Z= 0.173 Angle : 0.728 14.013 14774 Z= 0.350 Chirality : 0.054 0.496 1677 Planarity : 0.004 0.036 1508 Dihedral : 18.216 152.236 2313 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 1.70 % Allowed : 15.03 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.27), residues: 1009 helix: 1.33 (0.22), residues: 553 sheet: -1.16 (0.54), residues: 99 loop : -2.57 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 523 TYR 0.015 0.001 TYR A 700 PHE 0.024 0.002 PHE A 191 TRP 0.044 0.002 TRP A 377 HIS 0.005 0.001 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (10601) covalent geometry : angle 0.72759 / 0.35 (14774) hydrogen bonds : bond 0.03656 / 2.36 ( 517) hydrogen bonds : angle 3.82759 / 2.81 ( 1435) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2724.96 seconds wall clock time: 47 minutes 31.31 seconds (2851.31 seconds total)