Starting phenix.real_space_refine on Sun Apr 5 11:20:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w5c_21541/04_2026/6w5c_21541.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w5c_21541/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6w5c_21541/04_2026/6w5c_21541.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w5c_21541/04_2026/6w5c_21541.map" model { file = "/net/cci-nas-00/data/ceres_data/6w5c_21541/04_2026/6w5c_21541.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w5c_21541/04_2026/6w5c_21541.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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-2.1rc1-6017/lib/python3.9/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: {'RNA': 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: 2.51, per 1000 atoms: 0.25 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: 0.83 Conformation dependent library (CDL) restraints added in 437.7 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: 1.22 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: 2.51 Time building geometry restraints manager: 1.15 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=" N GLY A 789 " pdb=" CA GLY A 789 " ideal model delta sigma weight residual 1.449 1.481 -0.032 1.23e-02 6.61e+03 6.92e+00 bond pdb=" N SER A 167 " pdb=" CA SER A 167 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.31e-02 5.83e+03 6.90e+00 bond pdb=" N LYS A 790 " pdb=" CA LYS A 790 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.21e-02 6.83e+03 6.70e+00 ... (remaining 10596 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 14416 1.73 - 3.46: 293 3.46 - 5.18: 49 5.18 - 6.91: 9 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 - 35.31: 6028 35.31 - 70.62: 325 70.62 - 105.93: 21 105.93 - 141.24: 0 141.24 - 176.55: 4 Dihedral angle restraints: 6378 sinusoidal: 3369 harmonic: 3009 Sorted by residual: dihedral pdb=" O4' U B -19 " pdb=" C1' U B -19 " pdb=" N1 U B -19 " pdb=" C2 U B -19 " ideal model delta sinusoidal sigma weight residual 232.00 55.45 176.55 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B -6 " pdb=" C1' U B -6 " pdb=" N1 U B -6 " pdb=" C2 U B -6 " ideal model delta sinusoidal sigma weight residual -128.00 38.49 -166.49 1 1.70e+01 3.46e-03 6.55e+01 dihedral pdb=" O4' U B -21 " pdb=" C1' U B -21 " pdb=" N1 U B -21 " pdb=" C2 U B -21 " ideal model delta sinusoidal sigma weight residual -128.00 36.38 -164.38 1 1.70e+01 3.46e-03 6.52e+01 ... (remaining 6375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1342 0.044 - 0.088: 250 0.088 - 0.132: 76 0.132 - 0.176: 5 0.176 - 0.220: 4 Chirality restraints: 1677 Sorted by residual: chirality pdb=" CA PRO A 955 " pdb=" N PRO A 955 " pdb=" C PRO A 955 " pdb=" CB PRO A 955 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA PHE A 347 " pdb=" N PHE A 347 " pdb=" C PHE A 347 " pdb=" CB PHE A 347 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.58e-01 chirality pdb=" CA PRO A 987 " pdb=" N PRO A 987 " pdb=" C PRO A 987 " pdb=" CB PRO A 987 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.19 2.00e-01 2.50e+01 9.35e-01 ... (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: 0.170 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.530 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 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= 0.215 Angle : 0.637 8.640 14774 Z= 0.405 Chirality : 0.039 0.220 1677 Planarity : 0.003 0.039 1508 Dihedral : 18.523 176.553 4432 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 covalent geometry : bond 0.00389 (10601) covalent geometry : angle 0.63718 (14774) hydrogen bonds : bond 0.15168 ( 517) hydrogen bonds : angle 6.81617 ( 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 : 0.465 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: 0.6020 time to fit residues: 69.3662 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 : 0.363 ------------------------------------------------------------------------------- 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: 8.9990 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: 0.9990 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN A 459 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 = 0.3828 r_free = 0.3828 target = 0.122827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.089540 restraints weight = 16423.957| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.14 r_work: 0.3179 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10601 Z= 0.223 Angle : 0.615 10.029 14774 Z= 0.331 Chirality : 0.040 0.155 1677 Planarity : 0.004 0.075 1508 Dihedral : 21.342 176.445 2530 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 2.06 % Allowed : 10.06 % Favored : 87.88 % 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: -1.06 (0.26), residues: 1009 helix: 0.88 (0.22), residues: 554 sheet: -2.16 (0.51), residues: 99 loop : -2.88 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 652 TYR 0.017 0.002 TYR A 754 PHE 0.013 0.002 PHE A 476 TRP 0.019 0.002 TRP A 79 HIS 0.004 0.001 HIS A 711 Details of bonding type rmsd covalent geometry : bond 0.00508 (10601) covalent geometry : angle 0.61455 (14774) hydrogen bonds : bond 0.04143 ( 517) hydrogen bonds : angle 4.49223 ( 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 97 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.253 Fit side-chains REVERT: A 273 PHE cc_start: 0.7250 (m-80) cc_final: 0.6957 (m-80) REVERT: A 345 GLU cc_start: 0.8659 (tt0) cc_final: 0.8120 (mm-30) REVERT: A 450 ASP cc_start: 0.8113 (m-30) cc_final: 0.7735 (m-30) REVERT: A 740 MET cc_start: 0.6554 (mtp) cc_final: 0.6291 (mtm) REVERT: A 837 ILE cc_start: 0.8934 (mm) cc_final: 0.8707 (mp) outliers start: 17 outliers final: 5 residues processed: 90 average time/residue: 0.5351 time to fit residues: 52.0687 Evaluate side-chains 72 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 316 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 88 optimal weight: 3.9990 chunk 102 optimal weight: 20.0000 chunk 26 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 94 optimal weight: 40.0000 chunk 99 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 64 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 71 optimal weight: 0.0470 overall best weight: 1.5882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 190 GLN 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 = 0.3843 r_free = 0.3843 target = 0.124750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.091881 restraints weight = 16434.991| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.19 r_work: 0.3188 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10601 Z= 0.154 Angle : 0.549 8.804 14774 Z= 0.298 Chirality : 0.038 0.153 1677 Planarity : 0.004 0.071 1508 Dihedral : 21.171 179.620 2524 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 1.58 % Allowed : 9.94 % Favored : 88.48 % 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: 1.17 (0.22), residues: 550 sheet: -1.76 (0.52), residues: 99 loop : -2.77 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 26 TYR 0.012 0.001 TYR A 754 PHE 0.012 0.001 PHE A1090 TRP 0.020 0.002 TRP A 377 HIS 0.004 0.001 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00342 (10601) covalent geometry : angle 0.54870 (14774) hydrogen bonds : bond 0.03575 ( 517) hydrogen bonds : angle 4.07638 ( 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 96 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.376 Fit side-chains REVERT: A 153 LEU cc_start: 0.8709 (pp) cc_final: 0.8508 (pt) REVERT: A 273 PHE cc_start: 0.7514 (m-80) cc_final: 0.7284 (m-80) REVERT: A 386 LYS cc_start: 0.8301 (mtpp) cc_final: 0.8041 (mtmm) REVERT: A 450 ASP cc_start: 0.7932 (m-30) cc_final: 0.7595 (m-30) REVERT: A 776 LYS cc_start: 0.8857 (tmtt) cc_final: 0.8495 (tmmm) REVERT: A 913 MET cc_start: 0.8861 (mtm) cc_final: 0.8352 (mtm) REVERT: A 1046 MET cc_start: 0.7846 (ptp) cc_final: 0.7614 (mtm) outliers start: 13 outliers final: 4 residues processed: 92 average time/residue: 0.5094 time to fit residues: 51.1074 Evaluate side-chains 78 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.249 ------------------------------------------------------------------------------- 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 293 VAL Chi-restraints excluded: chain A residue 1059 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 106 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 101 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 84 optimal weight: 0.5980 chunk 86 optimal weight: 7.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 654 ASN A 942 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.122876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.089340 restraints weight = 16574.397| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.21 r_work: 0.3145 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10601 Z= 0.212 Angle : 0.573 7.711 14774 Z= 0.310 Chirality : 0.039 0.152 1677 Planarity : 0.004 0.070 1508 Dihedral : 21.139 178.775 2523 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 2.55 % Allowed : 11.52 % Favored : 85.94 % 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: -0.66 (0.27), residues: 1009 helix: 1.15 (0.22), residues: 552 sheet: -1.57 (0.49), residues: 107 loop : -2.72 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 26 TYR 0.011 0.002 TYR A 135 PHE 0.018 0.002 PHE A1090 TRP 0.024 0.002 TRP A 377 HIS 0.005 0.001 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00484 (10601) covalent geometry : angle 0.57267 (14774) hydrogen bonds : bond 0.03694 ( 517) hydrogen bonds : angle 4.04498 ( 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 95 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.364 Fit side-chains REVERT: A 273 PHE cc_start: 0.7532 (m-80) cc_final: 0.7271 (m-80) REVERT: A 412 GLN cc_start: 0.7825 (tp40) cc_final: 0.7412 (tm-30) REVERT: A 446 ASP cc_start: 0.7886 (p0) cc_final: 0.7640 (p0) REVERT: A 450 ASP cc_start: 0.7975 (m-30) cc_final: 0.7573 (m-30) REVERT: A 776 LYS cc_start: 0.8925 (tmtt) cc_final: 0.8574 (tmmm) REVERT: A 870 VAL cc_start: 0.9095 (OUTLIER) cc_final: 0.8777 (m) REVERT: A 1046 MET cc_start: 0.7834 (ptp) cc_final: 0.7596 (mtm) outliers start: 21 outliers final: 9 residues processed: 89 average time/residue: 0.5409 time to fit residues: 52.3048 Evaluate side-chains 81 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 TYR 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 838 THR Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1074 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 80 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 90 optimal weight: 20.0000 chunk 9 optimal weight: 0.2980 chunk 20 optimal weight: 50.0000 chunk 26 optimal weight: 0.8980 chunk 107 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 102 optimal weight: 20.0000 chunk 30 optimal weight: 7.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3887 r_free = 0.3887 target = 0.126680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.093771 restraints weight = 16533.319| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.17 r_work: 0.3259 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10601 Z= 0.126 Angle : 0.522 10.497 14774 Z= 0.281 Chirality : 0.036 0.137 1677 Planarity : 0.004 0.066 1508 Dihedral : 21.001 178.264 2523 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 1.58 % Allowed : 12.36 % Favored : 86.06 % 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: -0.34 (0.27), residues: 1009 helix: 1.39 (0.23), residues: 554 sheet: -1.31 (0.49), residues: 107 loop : -2.64 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 523 TYR 0.009 0.001 TYR A 36 PHE 0.016 0.001 PHE A1090 TRP 0.026 0.002 TRP A 377 HIS 0.004 0.001 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00271 (10601) covalent geometry : angle 0.52185 (14774) hydrogen bonds : bond 0.03279 ( 517) hydrogen bonds : angle 3.77325 ( 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 95 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.485 Fit side-chains REVERT: A 273 PHE cc_start: 0.7603 (m-80) cc_final: 0.7397 (m-80) REVERT: A 412 GLN cc_start: 0.7776 (tp40) cc_final: 0.7308 (tm-30) REVERT: A 450 ASP cc_start: 0.7957 (m-30) cc_final: 0.7622 (m-30) REVERT: A 718 PHE cc_start: 0.8662 (t80) cc_final: 0.8361 (t80) REVERT: A 776 LYS cc_start: 0.8932 (tmtt) cc_final: 0.8622 (tptp) REVERT: A 870 VAL cc_start: 0.8990 (OUTLIER) cc_final: 0.8748 (m) REVERT: A 873 ASN cc_start: 0.8168 (OUTLIER) cc_final: 0.7894 (t0) REVERT: A 913 MET cc_start: 0.8841 (mtm) cc_final: 0.8262 (mtm) REVERT: A 973 GLU cc_start: 0.8566 (tt0) cc_final: 0.8115 (mm-30) REVERT: A 1059 THR cc_start: 0.8473 (OUTLIER) cc_final: 0.7984 (p) outliers start: 13 outliers final: 4 residues processed: 91 average time/residue: 0.5706 time to fit residues: 56.0975 Evaluate side-chains 80 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1063 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 23 optimal weight: 20.0000 chunk 13 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 78 optimal weight: 0.7980 chunk 94 optimal weight: 40.0000 chunk 73 optimal weight: 0.0770 chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 overall best weight: 1.5342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3862 r_free = 0.3862 target = 0.125880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.092917 restraints weight = 16667.584| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.22 r_work: 0.3209 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10601 Z= 0.147 Angle : 0.524 8.439 14774 Z= 0.283 Chirality : 0.036 0.146 1677 Planarity : 0.003 0.034 1508 Dihedral : 21.025 179.657 2523 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 1.70 % Allowed : 14.06 % Favored : 84.24 % 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: -0.26 (0.27), residues: 1009 helix: 1.37 (0.22), residues: 561 sheet: -1.20 (0.49), residues: 107 loop : -2.52 (0.31), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 523 TYR 0.008 0.001 TYR A 36 PHE 0.016 0.001 PHE A1090 TRP 0.021 0.002 TRP A 377 HIS 0.004 0.001 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00328 (10601) covalent geometry : angle 0.52433 (14774) hydrogen bonds : bond 0.03293 ( 517) hydrogen bonds : angle 3.71915 ( 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 93 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.371 Fit side-chains REVERT: A 228 ARG cc_start: 0.5232 (ppt170) cc_final: 0.4865 (ppt170) REVERT: A 412 GLN cc_start: 0.7795 (tp40) cc_final: 0.7381 (tm-30) REVERT: A 446 ASP cc_start: 0.7899 (p0) cc_final: 0.7477 (p0) REVERT: A 450 ASP cc_start: 0.7946 (m-30) cc_final: 0.7602 (m-30) REVERT: A 693 LYS cc_start: 0.7670 (mtpt) cc_final: 0.7449 (pttt) REVERT: A 718 PHE cc_start: 0.8658 (t80) cc_final: 0.8345 (t80) REVERT: A 776 LYS cc_start: 0.8928 (tmtt) cc_final: 0.8605 (tptp) REVERT: A 870 VAL cc_start: 0.9029 (OUTLIER) cc_final: 0.8753 (m) REVERT: A 913 MET cc_start: 0.8852 (mtm) cc_final: 0.8366 (mtm) REVERT: A 973 GLU cc_start: 0.8587 (tt0) cc_final: 0.8119 (mm-30) REVERT: A 1059 THR cc_start: 0.8365 (OUTLIER) cc_final: 0.7977 (p) outliers start: 14 outliers final: 8 residues processed: 90 average time/residue: 0.5856 time to fit residues: 56.7213 Evaluate side-chains 83 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 TYR 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 664 ASN 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 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: 0.8980 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 43 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3841 r_free = 0.3841 target = 0.124413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.090933 restraints weight = 16469.617| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.21 r_work: 0.3175 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10601 Z= 0.187 Angle : 0.552 11.137 14774 Z= 0.296 Chirality : 0.038 0.148 1677 Planarity : 0.003 0.037 1508 Dihedral : 21.025 179.161 2523 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 2.30 % Allowed : 13.70 % 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: -0.26 (0.27), residues: 1009 helix: 1.34 (0.22), residues: 560 sheet: -1.17 (0.49), residues: 107 loop : -2.49 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 523 TYR 0.012 0.001 TYR A 135 PHE 0.021 0.002 PHE A1090 TRP 0.032 0.002 TRP A 377 HIS 0.005 0.001 HIS A 527 Details of bonding type rmsd covalent geometry : bond 0.00426 (10601) covalent geometry : angle 0.55206 (14774) hydrogen bonds : bond 0.03462 ( 517) hydrogen bonds : angle 3.78333 ( 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 97 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.337 Fit side-chains REVERT: A 228 ARG cc_start: 0.5092 (ppt170) cc_final: 0.4617 (ppt170) REVERT: A 412 GLN cc_start: 0.7811 (tp40) cc_final: 0.7386 (tm-30) REVERT: A 446 ASP cc_start: 0.8005 (p0) cc_final: 0.7704 (p0) REVERT: A 450 ASP cc_start: 0.7992 (m-30) cc_final: 0.7625 (m-30) REVERT: A 693 LYS cc_start: 0.7679 (mtpt) cc_final: 0.7395 (pttt) REVERT: A 776 LYS cc_start: 0.8941 (tmtt) cc_final: 0.8616 (tptp) REVERT: A 821 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8651 (tt) REVERT: A 870 VAL cc_start: 0.9070 (OUTLIER) cc_final: 0.8755 (m) REVERT: A 973 GLU cc_start: 0.8597 (tt0) cc_final: 0.8121 (mm-30) REVERT: A 1059 THR cc_start: 0.8380 (OUTLIER) cc_final: 0.7978 (p) outliers start: 19 outliers final: 11 residues processed: 92 average time/residue: 0.5976 time to fit residues: 59.3410 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 : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 TYR 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 821 LEU Chi-restraints excluded: chain A residue 870 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: 6.9990 chunk 76 optimal weight: 0.9990 chunk 11 optimal weight: 0.0870 chunk 55 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 654 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.124402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.090978 restraints weight = 16498.550| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.21 r_work: 0.3176 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2379 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= 0.183 Angle : 0.543 7.791 14774 Z= 0.293 Chirality : 0.038 0.148 1677 Planarity : 0.004 0.034 1508 Dihedral : 21.025 179.206 2523 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % 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: -0.27 (0.27), residues: 1009 helix: 1.33 (0.22), residues: 560 sheet: -1.10 (0.52), residues: 99 loop : -2.49 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 523 TYR 0.010 0.001 TYR A 996 PHE 0.018 0.002 PHE A1090 TRP 0.034 0.002 TRP A 377 HIS 0.005 0.001 HIS A 527 Details of bonding type rmsd covalent geometry : bond 0.00415 (10601) covalent geometry : angle 0.54263 (14774) hydrogen bonds : bond 0.03428 ( 517) hydrogen bonds : angle 3.79023 ( 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 95 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.354 Fit side-chains REVERT: A 228 ARG cc_start: 0.5162 (ppt170) cc_final: 0.4608 (ppt170) REVERT: A 412 GLN cc_start: 0.7816 (tp40) cc_final: 0.7387 (tm-30) REVERT: A 446 ASP cc_start: 0.8009 (p0) cc_final: 0.7705 (p0) REVERT: A 450 ASP cc_start: 0.8000 (m-30) cc_final: 0.7621 (m-30) REVERT: A 693 LYS cc_start: 0.7647 (mtpt) cc_final: 0.7439 (pttt) REVERT: A 821 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8647 (tt) REVERT: A 870 VAL cc_start: 0.9059 (OUTLIER) cc_final: 0.8758 (m) REVERT: A 913 MET cc_start: 0.8838 (mtm) cc_final: 0.8339 (mtp) REVERT: A 973 GLU cc_start: 0.8578 (tt0) cc_final: 0.8132 (mm-30) REVERT: A 1059 THR cc_start: 0.8382 (OUTLIER) cc_final: 0.7988 (p) outliers start: 17 outliers final: 10 residues processed: 90 average time/residue: 0.5682 time to fit residues: 55.2653 Evaluate side-chains 87 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 275 TYR 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 821 LEU Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 1059 THR 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: 8.9990 chunk 41 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 68 optimal weight: 0.0050 chunk 88 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 overall best weight: 1.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 654 ASN A1064 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 = 0.126249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.093279 restraints weight = 16534.831| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.21 r_work: 0.3213 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10601 Z= 0.139 Angle : 0.535 12.342 14774 Z= 0.286 Chirality : 0.037 0.144 1677 Planarity : 0.003 0.033 1508 Dihedral : 20.948 179.325 2523 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 1.94 % Allowed : 14.67 % 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: -0.17 (0.27), residues: 1009 helix: 1.42 (0.22), residues: 560 sheet: -1.03 (0.50), residues: 107 loop : -2.48 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 523 TYR 0.010 0.001 TYR A 996 PHE 0.016 0.001 PHE A1090 TRP 0.035 0.002 TRP A 377 HIS 0.005 0.001 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00310 (10601) covalent geometry : angle 0.53540 (14774) hydrogen bonds : bond 0.03269 ( 517) hydrogen bonds : angle 3.69640 ( 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 94 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.345 Fit side-chains REVERT: A 228 ARG cc_start: 0.4932 (ppt170) cc_final: 0.4399 (ppt170) REVERT: A 386 LYS cc_start: 0.8324 (mtpp) cc_final: 0.7994 (mtmm) REVERT: A 412 GLN cc_start: 0.7749 (tp40) cc_final: 0.7365 (tm-30) REVERT: A 446 ASP cc_start: 0.7979 (p0) cc_final: 0.7679 (p0) REVERT: A 450 ASP cc_start: 0.7996 (m-30) cc_final: 0.7612 (m-30) REVERT: A 718 PHE cc_start: 0.8655 (t80) cc_final: 0.8354 (t80) REVERT: A 821 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8705 (tt) REVERT: A 870 VAL cc_start: 0.9016 (OUTLIER) cc_final: 0.8745 (m) REVERT: A 913 MET cc_start: 0.8780 (mtm) cc_final: 0.8254 (mtp) REVERT: A 973 GLU cc_start: 0.8545 (tt0) cc_final: 0.8109 (mm-30) REVERT: A 1059 THR cc_start: 0.8360 (OUTLIER) cc_final: 0.8055 (p) outliers start: 16 outliers final: 10 residues processed: 90 average time/residue: 0.5380 time to fit residues: 52.6616 Evaluate side-chains 86 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 275 TYR 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 371 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 1059 THR 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: 8.9990 chunk 62 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 19 optimal weight: 20.0000 chunk 41 optimal weight: 6.9990 chunk 110 optimal weight: 20.0000 chunk 56 optimal weight: 7.9990 chunk 34 optimal weight: 0.5980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 654 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.124197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.090850 restraints weight = 16395.277| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.20 r_work: 0.3178 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10601 Z= 0.198 Angle : 0.559 7.410 14774 Z= 0.301 Chirality : 0.038 0.148 1677 Planarity : 0.004 0.035 1508 Dihedral : 21.005 179.420 2523 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 1.82 % Allowed : 15.03 % Favored : 83.15 % 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: -0.23 (0.27), residues: 1009 helix: 1.34 (0.22), residues: 561 sheet: -1.07 (0.50), residues: 107 loop : -2.46 (0.31), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 523 TYR 0.010 0.001 TYR A 135 PHE 0.021 0.002 PHE A1090 TRP 0.043 0.002 TRP A 377 HIS 0.006 0.001 HIS A 527 Details of bonding type rmsd covalent geometry : bond 0.00453 (10601) covalent geometry : angle 0.55890 (14774) hydrogen bonds : bond 0.03478 ( 517) hydrogen bonds : angle 3.77197 ( 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 93 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.361 Fit side-chains REVERT: A 228 ARG cc_start: 0.4961 (ppt170) cc_final: 0.4451 (ppt170) REVERT: A 389 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7596 (mt-10) REVERT: A 412 GLN cc_start: 0.7813 (tp40) cc_final: 0.7397 (tm-30) REVERT: A 446 ASP cc_start: 0.7999 (p0) cc_final: 0.7704 (p0) REVERT: A 450 ASP cc_start: 0.8006 (m-30) cc_final: 0.7620 (m-30) REVERT: A 531 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8494 (mt) REVERT: A 821 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8662 (tt) REVERT: A 870 VAL cc_start: 0.9068 (OUTLIER) cc_final: 0.8756 (m) REVERT: A 913 MET cc_start: 0.8791 (mtm) cc_final: 0.8257 (mtp) REVERT: A 973 GLU cc_start: 0.8553 (tt0) cc_final: 0.8128 (mm-30) REVERT: A 1059 THR cc_start: 0.8391 (OUTLIER) cc_final: 0.8051 (p) outliers start: 15 outliers final: 9 residues processed: 89 average time/residue: 0.5568 time to fit residues: 53.7632 Evaluate side-chains 87 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 275 TYR 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 531 LEU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 1059 THR 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: 6.9990 chunk 74 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 94 optimal weight: 50.0000 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3850 r_free = 0.3850 target = 0.124855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.091575 restraints weight = 16478.453| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.20 r_work: 0.3187 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2514 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 : 0.556 12.322 14774 Z= 0.298 Chirality : 0.038 0.147 1677 Planarity : 0.003 0.034 1508 Dihedral : 20.987 179.385 2523 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 2.06 % Allowed : 15.15 % Favored : 82.79 % 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: -0.24 (0.27), residues: 1009 helix: 1.36 (0.22), residues: 559 sheet: -1.08 (0.50), residues: 107 loop : -2.48 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 523 TYR 0.009 0.001 TYR A 135 PHE 0.020 0.001 PHE A1090 TRP 0.043 0.002 TRP A 377 HIS 0.006 0.001 HIS A 527 Details of bonding type rmsd covalent geometry : bond 0.00395 (10601) covalent geometry : angle 0.55631 (14774) hydrogen bonds : bond 0.03409 ( 517) hydrogen bonds : angle 3.77593 ( 1435) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2863.68 seconds wall clock time: 49 minutes 51.80 seconds (2991.80 seconds total)