Starting phenix.real_space_refine on Mon Jul 28 06:37:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w5c_21541/07_2025/6w5c_21541.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w5c_21541/07_2025/6w5c_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_21541/07_2025/6w5c_21541.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w5c_21541/07_2025/6w5c_21541.map" model { file = "/net/cci-nas-00/data/ceres_data/6w5c_21541/07_2025/6w5c_21541.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w5c_21541/07_2025/6w5c_21541.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 10, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 4} 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: 6.40, per 1000 atoms: 0.63 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: 2.52 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 3.61 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: 5.62 Time building geometry restraints manager: 3.01 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: 0.300 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 30.280 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:16.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.670 ------------------------------------------------------------------------------- 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 : 8.53 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (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 TRP 0.017 0.002 TRP A 79 HIS 0.003 0.001 HIS A 711 PHE 0.009 0.001 PHE A 536 TYR 0.042 0.002 TYR A 754 ARG 0.003 0.000 ARG A 652 Details of bonding type rmsd hydrogen bonds : bond 0.15168 ( 517) hydrogen bonds : angle 6.81617 ( 1435) covalent geometry : bond 0.00389 (10601) covalent geometry : angle 0.63718 (14774) *********************** 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 : 0.998 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 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: 1.2132 time to fit residues: 140.2834 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 : 1.002 ------------------------------------------------------------------------------- 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 93 optimal weight: 8.9990 chunk 84 optimal weight: 0.5980 chunk 46 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 = 0.3842 r_free = 0.3842 target = 0.124080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.090606 restraints weight = 16319.950| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.16 r_work: 0.3205 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1381 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= 0.167 Angle : 0.588 9.977 14774 Z= 0.317 Chirality : 0.039 0.159 1677 Planarity : 0.004 0.072 1508 Dihedral : 21.305 178.026 2530 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 2.06 % Allowed : 9.70 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.27), residues: 1009 helix: 1.10 (0.23), residues: 548 sheet: -2.17 (0.48), residues: 107 loop : -2.83 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 79 HIS 0.004 0.001 HIS A 366 PHE 0.012 0.001 PHE A 348 TYR 0.018 0.002 TYR A 754 ARG 0.007 0.001 ARG A 652 Details of bonding type rmsd hydrogen bonds : bond 0.03874 ( 517) hydrogen bonds : angle 4.38138 ( 1435) covalent geometry : bond 0.00372 (10601) covalent geometry : angle 0.58781 (14774) *********************** 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 99 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 1.021 Fit side-chains REVERT: A 273 PHE cc_start: 0.7249 (m-80) cc_final: 0.6977 (m-80) REVERT: A 345 GLU cc_start: 0.8578 (tt0) cc_final: 0.8215 (mm-30) REVERT: A 450 ASP cc_start: 0.8053 (m-30) cc_final: 0.7664 (m-30) outliers start: 17 outliers final: 4 residues processed: 92 average time/residue: 1.1233 time to fit residues: 113.1374 Evaluate side-chains 73 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 1.040 ------------------------------------------------------------------------------- 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 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 42 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 = 0.3800 r_free = 0.3800 target = 0.121930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.088327 restraints weight = 16584.659| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.21 r_work: 0.3130 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 10601 Z= 0.248 Angle : 0.614 9.309 14774 Z= 0.330 Chirality : 0.041 0.173 1677 Planarity : 0.004 0.074 1508 Dihedral : 21.257 178.365 2524 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 1.82 % Allowed : 10.67 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.26), residues: 1009 helix: 1.05 (0.22), residues: 548 sheet: -1.93 (0.48), residues: 107 loop : -2.78 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 377 HIS 0.005 0.001 HIS A 366 PHE 0.016 0.002 PHE A1090 TYR 0.012 0.002 TYR A 754 ARG 0.005 0.001 ARG A 26 Details of bonding type rmsd hydrogen bonds : bond 0.03971 ( 517) hydrogen bonds : angle 4.26144 ( 1435) covalent geometry : bond 0.00567 (10601) covalent geometry : angle 0.61379 (14774) *********************** 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 93 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.974 Fit side-chains REVERT: A 345 GLU cc_start: 0.8488 (tt0) cc_final: 0.8192 (mm-30) REVERT: A 450 ASP cc_start: 0.7891 (m-30) cc_final: 0.7510 (m-30) REVERT: A 837 ILE cc_start: 0.8921 (mm) cc_final: 0.8712 (mp) REVERT: A 1088 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8261 (mttp) outliers start: 15 outliers final: 7 residues processed: 89 average time/residue: 1.1271 time to fit residues: 109.5331 Evaluate side-chains 77 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 1.049 ------------------------------------------------------------------------------- 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 293 VAL Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 316 THR 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 9 optimal weight: 0.9990 chunk 86 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 22 optimal weight: 0.0060 chunk 88 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 overall best weight: 0.7400 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.127582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.095204 restraints weight = 16490.070| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.15 r_work: 0.3271 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10601 Z= 0.122 Angle : 0.525 9.977 14774 Z= 0.285 Chirality : 0.036 0.136 1677 Planarity : 0.004 0.070 1508 Dihedral : 21.051 177.552 2524 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 1.33 % Allowed : 12.00 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.27), residues: 1009 helix: 1.33 (0.23), residues: 553 sheet: -1.44 (0.52), residues: 99 loop : -2.66 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 377 HIS 0.004 0.001 HIS A 366 PHE 0.024 0.001 PHE A 191 TYR 0.009 0.001 TYR A 36 ARG 0.004 0.000 ARG A 26 Details of bonding type rmsd hydrogen bonds : bond 0.03339 ( 517) hydrogen bonds : angle 3.84302 ( 1435) covalent geometry : bond 0.00259 (10601) covalent geometry : angle 0.52530 (14774) *********************** 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 97 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.807 Fit side-chains REVERT: A 273 PHE cc_start: 0.7574 (m-80) cc_final: 0.7339 (m-80) REVERT: A 450 ASP cc_start: 0.7934 (m-30) cc_final: 0.7562 (m-30) REVERT: A 776 LYS cc_start: 0.8923 (tmtt) cc_final: 0.8523 (tmmm) REVERT: A 870 VAL cc_start: 0.9019 (OUTLIER) cc_final: 0.8791 (m) REVERT: A 873 ASN cc_start: 0.8210 (OUTLIER) cc_final: 0.7918 (t0) REVERT: A 913 MET cc_start: 0.8799 (mtm) cc_final: 0.8172 (mtm) REVERT: A 1059 THR cc_start: 0.8494 (OUTLIER) cc_final: 0.8016 (p) outliers start: 11 outliers final: 4 residues processed: 95 average time/residue: 1.2691 time to fit residues: 130.7661 Evaluate side-chains 77 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL 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 1009 LEU Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1063 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 109 optimal weight: 8.9990 chunk 5 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 50.0000 chunk 97 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 654 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.123202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.089869 restraints weight = 16514.172| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.20 r_work: 0.3154 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10601 Z= 0.224 Angle : 0.572 7.715 14774 Z= 0.307 Chirality : 0.040 0.158 1677 Planarity : 0.004 0.040 1508 Dihedral : 21.096 179.146 2523 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 1.82 % Allowed : 13.33 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.27), residues: 1009 helix: 1.21 (0.22), residues: 555 sheet: -1.57 (0.49), residues: 109 loop : -2.57 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 377 HIS 0.005 0.001 HIS A 527 PHE 0.024 0.002 PHE A 191 TYR 0.012 0.002 TYR A 135 ARG 0.005 0.001 ARG A 523 Details of bonding type rmsd hydrogen bonds : bond 0.03653 ( 517) hydrogen bonds : angle 3.93946 ( 1435) covalent geometry : bond 0.00510 (10601) covalent geometry : angle 0.57198 (14774) *********************** 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 97 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.944 Fit side-chains REVERT: A 273 PHE cc_start: 0.7596 (m-80) cc_final: 0.7369 (m-80) REVERT: A 412 GLN cc_start: 0.7822 (tp40) cc_final: 0.7399 (tm-30) REVERT: A 870 VAL cc_start: 0.9091 (OUTLIER) cc_final: 0.8769 (m) outliers start: 15 outliers final: 6 residues processed: 93 average time/residue: 1.2215 time to fit residues: 123.1508 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 : 0.993 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 104 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 = 0.124449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.091286 restraints weight = 16483.569| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.20 r_work: 0.3184 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10601 Z= 0.173 Angle : 0.550 9.118 14774 Z= 0.295 Chirality : 0.038 0.147 1677 Planarity : 0.003 0.033 1508 Dihedral : 21.058 179.571 2523 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 2.18 % Allowed : 13.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.27), residues: 1009 helix: 1.27 (0.22), residues: 553 sheet: -1.31 (0.49), residues: 107 loop : -2.61 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 377 HIS 0.004 0.001 HIS A 366 PHE 0.023 0.002 PHE A 191 TYR 0.013 0.001 TYR A 646 ARG 0.004 0.000 ARG A 523 Details of bonding type rmsd hydrogen bonds : bond 0.03446 ( 517) hydrogen bonds : angle 3.84561 ( 1435) covalent geometry : bond 0.00391 (10601) covalent geometry : angle 0.55037 (14774) *********************** 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 99 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 1.059 Fit side-chains REVERT: A 228 ARG cc_start: 0.5233 (ppt170) cc_final: 0.5025 (ppt170) REVERT: A 273 PHE cc_start: 0.7619 (m-80) cc_final: 0.7394 (m-80) REVERT: A 412 GLN cc_start: 0.7817 (tp40) cc_final: 0.7396 (tm-30) REVERT: A 446 ASP cc_start: 0.7954 (p0) cc_final: 0.7705 (p0) REVERT: A 450 ASP cc_start: 0.7954 (m-30) cc_final: 0.7554 (m-30) REVERT: A 821 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8635 (tt) REVERT: A 870 VAL cc_start: 0.9060 (OUTLIER) cc_final: 0.8765 (m) REVERT: A 913 MET cc_start: 0.8823 (mtm) cc_final: 0.8376 (mtp) REVERT: A 973 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8028 (mm-30) REVERT: A 1059 THR cc_start: 0.8519 (OUTLIER) cc_final: 0.7956 (p) outliers start: 18 outliers final: 9 residues processed: 93 average time/residue: 1.3306 time to fit residues: 133.8055 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 : 1.023 ------------------------------------------------------------------------------- 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 445 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 973 GLU 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 3 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3874 r_free = 0.3874 target = 0.126575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.093524 restraints weight = 16752.135| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.23 r_work: 0.3224 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2520 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= 0.133 Angle : 0.527 9.081 14774 Z= 0.282 Chirality : 0.036 0.143 1677 Planarity : 0.003 0.032 1508 Dihedral : 20.947 179.143 2523 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 1.70 % Allowed : 14.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.27), residues: 1009 helix: 1.36 (0.22), residues: 561 sheet: -1.06 (0.53), residues: 99 loop : -2.53 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 377 HIS 0.004 0.001 HIS A 366 PHE 0.020 0.001 PHE A 191 TYR 0.012 0.001 TYR A 646 ARG 0.005 0.000 ARG A 523 Details of bonding type rmsd hydrogen bonds : bond 0.03233 ( 517) hydrogen bonds : angle 3.68769 ( 1435) covalent geometry : bond 0.00293 (10601) covalent geometry : angle 0.52706 (14774) *********************** 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 95 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 1.101 Fit side-chains REVERT: A 153 LEU cc_start: 0.8395 (pp) cc_final: 0.8167 (pt) REVERT: A 228 ARG cc_start: 0.5297 (ppt170) cc_final: 0.4744 (ppt170) REVERT: A 386 LYS cc_start: 0.8319 (mtpp) cc_final: 0.8047 (mtmm) REVERT: A 412 GLN cc_start: 0.7780 (tp40) cc_final: 0.7369 (tm-30) REVERT: A 446 ASP cc_start: 0.8001 (p0) cc_final: 0.7761 (p0) REVERT: A 450 ASP cc_start: 0.7979 (m-30) cc_final: 0.7596 (m-30) REVERT: A 693 LYS cc_start: 0.7771 (mtpt) cc_final: 0.7538 (pttt) REVERT: A 776 LYS cc_start: 0.8934 (tmtt) cc_final: 0.8583 (tptp) REVERT: A 844 LYS cc_start: 0.8277 (ttpp) cc_final: 0.8000 (tmmt) REVERT: A 870 VAL cc_start: 0.9009 (OUTLIER) cc_final: 0.8746 (m) REVERT: A 913 MET cc_start: 0.8789 (mtm) cc_final: 0.8344 (mtp) REVERT: A 973 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8028 (mm-30) REVERT: A 1059 THR cc_start: 0.8502 (m) cc_final: 0.8065 (p) outliers start: 14 outliers final: 9 residues processed: 92 average time/residue: 1.3232 time to fit residues: 132.0868 Evaluate side-chains 88 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 1.301 ------------------------------------------------------------------------------- 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 275 TYR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 445 VAL 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 973 GLU 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 64 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 102 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 48 optimal weight: 8.9990 chunk 97 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 overall best weight: 4.2386 ------------------------------------------------------------------------------- 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 A1062 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.121933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.088390 restraints weight = 16597.641| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.21 r_work: 0.3129 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 10601 Z= 0.276 Angle : 0.612 7.968 14774 Z= 0.327 Chirality : 0.042 0.166 1677 Planarity : 0.004 0.036 1508 Dihedral : 21.121 179.298 2523 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 2.79 % Allowed : 13.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.27), residues: 1009 helix: 1.10 (0.22), residues: 560 sheet: -1.41 (0.49), residues: 109 loop : -2.50 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 377 HIS 0.006 0.001 HIS A 527 PHE 0.022 0.002 PHE A 191 TYR 0.022 0.002 TYR A 646 ARG 0.008 0.001 ARG A 523 Details of bonding type rmsd hydrogen bonds : bond 0.03800 ( 517) hydrogen bonds : angle 3.94735 ( 1435) covalent geometry : bond 0.00634 (10601) covalent geometry : angle 0.61224 (14774) *********************** 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 104 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.932 Fit side-chains REVERT: A 228 ARG cc_start: 0.5179 (ppt170) cc_final: 0.4620 (ppt170) REVERT: A 370 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8235 (pm20) REVERT: A 412 GLN cc_start: 0.7829 (tp40) cc_final: 0.7462 (tm-30) REVERT: A 446 ASP cc_start: 0.8005 (p0) cc_final: 0.7784 (p0) REVERT: A 450 ASP cc_start: 0.7999 (m-30) cc_final: 0.7615 (m-30) REVERT: A 693 LYS cc_start: 0.7760 (mtpt) cc_final: 0.7432 (pttt) REVERT: A 776 LYS cc_start: 0.8940 (tmtt) cc_final: 0.8680 (tptp) REVERT: A 821 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8680 (tt) REVERT: A 870 VAL cc_start: 0.9121 (OUTLIER) cc_final: 0.8785 (m) REVERT: A 913 MET cc_start: 0.8828 (mtm) cc_final: 0.8233 (mtm) REVERT: A 973 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8031 (mm-30) REVERT: A 1001 MET cc_start: 0.8080 (mmm) cc_final: 0.7820 (mpp) REVERT: A 1059 THR cc_start: 0.8516 (m) cc_final: 0.7938 (p) REVERT: A 1062 ASN cc_start: 0.8432 (OUTLIER) cc_final: 0.8094 (m-40) outliers start: 23 outliers final: 14 residues processed: 99 average time/residue: 1.1789 time to fit residues: 126.3154 Evaluate side-chains 96 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 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 370 GLU 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 838 THR Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 928 VAL Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1062 ASN 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 12 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 72 optimal weight: 0.4980 chunk 73 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 94 optimal weight: 50.0000 chunk 0 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 A 654 ASN A1064 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.127213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.094621 restraints weight = 16477.023| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.20 r_work: 0.3239 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10601 Z= 0.122 Angle : 0.534 9.807 14774 Z= 0.286 Chirality : 0.036 0.141 1677 Planarity : 0.003 0.033 1508 Dihedral : 20.965 177.777 2523 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 1.33 % Allowed : 15.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.27), residues: 1009 helix: 1.38 (0.22), residues: 561 sheet: -1.05 (0.53), residues: 99 loop : -2.53 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 377 HIS 0.004 0.001 HIS A 366 PHE 0.021 0.001 PHE A 191 TYR 0.013 0.001 TYR A 646 ARG 0.008 0.001 ARG A 26 Details of bonding type rmsd hydrogen bonds : bond 0.03216 ( 517) hydrogen bonds : angle 3.68922 ( 1435) covalent geometry : bond 0.00265 (10601) covalent geometry : angle 0.53362 (14774) *********************** 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 97 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 1.309 Fit side-chains REVERT: A 228 ARG cc_start: 0.5227 (ppt170) cc_final: 0.4657 (ppt170) REVERT: A 386 LYS cc_start: 0.8322 (mtpp) cc_final: 0.7949 (mtmm) REVERT: A 412 GLN cc_start: 0.7783 (tp40) cc_final: 0.7369 (tm-30) REVERT: A 446 ASP cc_start: 0.7963 (p0) cc_final: 0.7718 (p0) REVERT: A 450 ASP cc_start: 0.7998 (m-30) cc_final: 0.7618 (m-30) REVERT: A 693 LYS cc_start: 0.7768 (mtpt) cc_final: 0.7547 (pttt) REVERT: A 776 LYS cc_start: 0.8908 (tmtt) cc_final: 0.8554 (tptp) REVERT: A 870 VAL cc_start: 0.8958 (OUTLIER) cc_final: 0.8732 (m) REVERT: A 913 MET cc_start: 0.8753 (mtm) cc_final: 0.8305 (mtp) REVERT: A 973 GLU cc_start: 0.8456 (tt0) cc_final: 0.8046 (mm-30) REVERT: A 1001 MET cc_start: 0.8078 (mmm) cc_final: 0.7831 (mpp) REVERT: A 1059 THR cc_start: 0.8512 (OUTLIER) cc_final: 0.8089 (p) REVERT: A 1085 ASP cc_start: 0.6986 (m-30) cc_final: 0.6637 (t70) outliers start: 11 outliers final: 7 residues processed: 94 average time/residue: 1.1880 time to fit residues: 121.8375 Evaluate side-chains 89 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU 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 445 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 9 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 67 optimal weight: 0.2980 chunk 103 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 98 optimal weight: 7.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 A1062 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.127171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.094137 restraints weight = 16554.428| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.22 r_work: 0.3238 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10601 Z= 0.130 Angle : 0.539 12.304 14774 Z= 0.286 Chirality : 0.036 0.168 1677 Planarity : 0.003 0.036 1508 Dihedral : 20.932 179.474 2523 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 1.58 % Allowed : 15.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.27), residues: 1009 helix: 1.48 (0.22), residues: 561 sheet: -1.00 (0.52), residues: 99 loop : -2.48 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 377 HIS 0.004 0.001 HIS A 366 PHE 0.028 0.002 PHE A 718 TYR 0.015 0.001 TYR A 646 ARG 0.008 0.000 ARG A 523 Details of bonding type rmsd hydrogen bonds : bond 0.03213 ( 517) hydrogen bonds : angle 3.62384 ( 1435) covalent geometry : bond 0.00289 (10601) covalent geometry : angle 0.53909 (14774) ********************** 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 100 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 3.205 Fit side-chains REVERT: A 160 LYS cc_start: 0.8710 (mmpt) cc_final: 0.8492 (mmpt) REVERT: A 228 ARG cc_start: 0.5128 (ppt170) cc_final: 0.4572 (ppt170) REVERT: A 389 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7604 (mt-10) REVERT: A 412 GLN cc_start: 0.7795 (tp40) cc_final: 0.7388 (tm-30) REVERT: A 446 ASP cc_start: 0.7972 (p0) cc_final: 0.7750 (p0) REVERT: A 450 ASP cc_start: 0.8006 (m-30) cc_final: 0.7636 (m-30) REVERT: A 776 LYS cc_start: 0.8924 (tmtt) cc_final: 0.8582 (tptp) REVERT: A 844 LYS cc_start: 0.8354 (ttpp) cc_final: 0.8008 (tmmt) REVERT: A 870 VAL cc_start: 0.9005 (OUTLIER) cc_final: 0.8751 (m) REVERT: A 913 MET cc_start: 0.8787 (mtm) cc_final: 0.8059 (mtm) REVERT: A 973 GLU cc_start: 0.8448 (tt0) cc_final: 0.8058 (mm-30) REVERT: A 1001 MET cc_start: 0.8146 (mmm) cc_final: 0.7924 (mpp) REVERT: A 1059 THR cc_start: 0.8453 (OUTLIER) cc_final: 0.8061 (p) REVERT: A 1085 ASP cc_start: 0.7032 (m-30) cc_final: 0.6669 (t70) outliers start: 13 outliers final: 6 residues processed: 95 average time/residue: 1.8995 time to fit residues: 196.4376 Evaluate side-chains 90 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 1.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU 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 445 VAL 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 102 optimal weight: 20.0000 chunk 90 optimal weight: 20.0000 chunk 21 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 A1062 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 = 0.123789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.090269 restraints weight = 16491.823| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.20 r_work: 0.3163 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10601 Z= 0.222 Angle : 0.579 7.782 14774 Z= 0.310 Chirality : 0.040 0.150 1677 Planarity : 0.004 0.036 1508 Dihedral : 21.023 179.962 2523 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 1.33 % Allowed : 16.00 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.27), residues: 1009 helix: 1.31 (0.22), residues: 560 sheet: -1.15 (0.50), residues: 107 loop : -2.48 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP A 377 HIS 0.006 0.001 HIS A 527 PHE 0.025 0.002 PHE A 718 TYR 0.019 0.002 TYR A 646 ARG 0.009 0.001 ARG A 523 Details of bonding type rmsd hydrogen bonds : bond 0.03558 ( 517) hydrogen bonds : angle 3.78950 ( 1435) covalent geometry : bond 0.00510 (10601) covalent geometry : angle 0.57850 (14774) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6807.68 seconds wall clock time: 124 minutes 52.52 seconds (7492.52 seconds total)