Starting phenix.real_space_refine on Fri Feb 14 10:49:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6w5c_21541/02_2025/6w5c_21541.cif Found real_map, /net/cci-nas-00/data/ceres_data/6w5c_21541/02_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_21541/02_2025/6w5c_21541.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6w5c_21541/02_2025/6w5c_21541.map" model { file = "/net/cci-nas-00/data/ceres_data/6w5c_21541/02_2025/6w5c_21541.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6w5c_21541/02_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-5592/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: 6.18, per 1000 atoms: 0.61 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: 2.78 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: 4.00 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: 5.56 Time building geometry restraints manager: 3.11 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: 0.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 29.720 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:11.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.120 ------------------------------------------------------------------------------- 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= 0.240 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 *********************** 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 : 0.886 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: 1.2935 time to fit residues: 149.5687 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 : 1.195 ------------------------------------------------------------------------------- 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 = 0.090604 restraints weight = 16319.950| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.16 r_work: 0.3205 rms_B_bonded: 3.13 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: 0.8122 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= 0.233 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 *********************** 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 : 1.011 Fit side-chains REVERT: A 273 PHE cc_start: 0.7254 (m-80) cc_final: 0.6981 (m-80) REVERT: A 345 GLU cc_start: 0.8579 (tt0) cc_final: 0.8217 (mm-30) REVERT: A 450 ASP cc_start: 0.8055 (m-30) cc_final: 0.7666 (m-30) outliers start: 17 outliers final: 4 residues processed: 92 average time/residue: 1.1019 time to fit residues: 110.9255 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 : 0.975 ------------------------------------------------------------------------------- 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: 5.9990 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: 1.9990 chunk 78 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3810 r_free = 0.3810 target = 0.122597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.089169 restraints weight = 16608.009| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.21 r_work: 0.3146 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1701 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= 0.314 Angle : 0.595 9.448 14774 Z= 0.320 Chirality : 0.040 0.151 1677 Planarity : 0.004 0.072 1508 Dihedral : 21.212 177.702 2524 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 1.82 % Allowed : 10.42 % Favored : 87.76 % 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: -0.77 (0.27), residues: 1009 helix: 1.11 (0.22), residues: 548 sheet: -1.87 (0.49), residues: 107 loop : -2.74 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 377 HIS 0.005 0.001 HIS A 366 PHE 0.015 0.002 PHE A1090 TYR 0.013 0.002 TYR A 754 ARG 0.005 0.001 ARG A 26 *********************** 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 92 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 1.154 Fit side-chains REVERT: A 345 GLU cc_start: 0.8438 (tt0) cc_final: 0.8199 (mm-30) REVERT: A 450 ASP cc_start: 0.7886 (m-30) cc_final: 0.7509 (m-30) REVERT: A 837 ILE cc_start: 0.8920 (mm) cc_final: 0.8707 (mp) REVERT: A 1046 MET cc_start: 0.7772 (ptp) cc_final: 0.7569 (mtm) REVERT: A 1088 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.7993 (mttp) outliers start: 15 outliers final: 7 residues processed: 88 average time/residue: 1.0691 time to fit residues: 103.3898 Evaluate side-chains 75 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 1.129 ------------------------------------------------------------------------------- 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: 0.9980 chunk 86 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 62 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 96 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 A 942 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.125907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.093235 restraints weight = 16485.976| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.21 r_work: 0.3214 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10601 Z= 0.178 Angle : 0.529 9.196 14774 Z= 0.287 Chirality : 0.036 0.140 1677 Planarity : 0.004 0.071 1508 Dihedral : 21.073 178.985 2524 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 1.70 % Allowed : 12.00 % Favored : 86.30 % 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: 1.30 (0.22), residues: 554 sheet: -1.46 (0.49), residues: 107 loop : -2.64 (0.31), residues: 348 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 0.013 0.001 PHE A1090 TYR 0.009 0.001 TYR A 36 ARG 0.005 0.000 ARG A 26 *********************** 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 96 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.925 Fit side-chains REVERT: A 273 PHE cc_start: 0.7513 (m-80) cc_final: 0.7270 (m-80) REVERT: A 450 ASP cc_start: 0.7946 (m-30) cc_final: 0.7531 (m-30) REVERT: A 776 LYS cc_start: 0.8921 (tmtt) cc_final: 0.8565 (tmmm) REVERT: A 870 VAL cc_start: 0.9000 (OUTLIER) cc_final: 0.8738 (m) REVERT: A 913 MET cc_start: 0.8827 (mtm) cc_final: 0.8174 (mtm) REVERT: A 1059 THR cc_start: 0.8479 (OUTLIER) cc_final: 0.7922 (p) outliers start: 14 outliers final: 5 residues processed: 92 average time/residue: 1.1809 time to fit residues: 117.8855 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 : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 870 VAL 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: 0.3980 chunk 26 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 40.0000 chunk 97 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 overall best weight: 2.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3832 r_free = 0.3832 target = 0.123981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.090478 restraints weight = 16490.087| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.21 r_work: 0.3166 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10601 Z= 0.280 Angle : 0.557 8.199 14774 Z= 0.300 Chirality : 0.038 0.149 1677 Planarity : 0.004 0.039 1508 Dihedral : 21.078 178.626 2523 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 2.30 % Allowed : 12.36 % Favored : 85.33 % 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: 1.27 (0.22), residues: 554 sheet: -1.35 (0.49), residues: 107 loop : -2.59 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 377 HIS 0.006 0.001 HIS A 527 PHE 0.019 0.002 PHE A1090 TYR 0.010 0.001 TYR A 135 ARG 0.005 0.001 ARG A 523 *********************** 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 98 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.979 Fit side-chains REVERT: A 228 ARG cc_start: 0.5237 (ppt170) cc_final: 0.5012 (ppt170) REVERT: A 273 PHE cc_start: 0.7599 (m-80) cc_final: 0.7361 (m-80) REVERT: A 412 GLN cc_start: 0.7820 (tp40) cc_final: 0.7408 (tm-30) REVERT: A 446 ASP cc_start: 0.7938 (p0) cc_final: 0.7630 (p0) REVERT: A 450 ASP cc_start: 0.7915 (m-30) cc_final: 0.7542 (m-30) REVERT: A 870 VAL cc_start: 0.9070 (OUTLIER) cc_final: 0.8755 (m) REVERT: A 913 MET cc_start: 0.8850 (mtm) cc_final: 0.8319 (mtm) REVERT: A 973 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8012 (mm-30) REVERT: A 1059 THR cc_start: 0.8473 (OUTLIER) cc_final: 0.7900 (p) outliers start: 19 outliers final: 9 residues processed: 92 average time/residue: 1.1459 time to fit residues: 114.7188 Evaluate side-chains 87 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 515 LYS 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 104 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 91 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.3867 r_free = 0.3867 target = 0.126245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.093174 restraints weight = 16490.364| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.21 r_work: 0.3214 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2382 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= 0.190 Angle : 0.525 9.135 14774 Z= 0.282 Chirality : 0.036 0.142 1677 Planarity : 0.003 0.032 1508 Dihedral : 20.974 179.158 2523 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 2.06 % Allowed : 12.85 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.27 (0.27), residues: 1009 helix: 1.42 (0.22), residues: 555 sheet: -1.13 (0.52), residues: 99 loop : -2.59 (0.30), residues: 355 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 0.013 0.001 PHE A1090 TYR 0.010 0.001 TYR A 996 ARG 0.006 0.000 ARG A 523 *********************** 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 97 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 1.079 Fit side-chains REVERT: A 228 ARG cc_start: 0.5239 (ppt170) cc_final: 0.4868 (ppt170) REVERT: A 273 PHE cc_start: 0.7637 (m-80) cc_final: 0.7435 (m-80) REVERT: A 412 GLN cc_start: 0.7785 (tp40) cc_final: 0.7357 (tm-30) REVERT: A 450 ASP cc_start: 0.7979 (m-30) cc_final: 0.7579 (m-30) REVERT: A 693 LYS cc_start: 0.7673 (mtpt) cc_final: 0.7381 (pttt) REVERT: A 870 VAL cc_start: 0.9015 (OUTLIER) cc_final: 0.8740 (m) REVERT: A 913 MET cc_start: 0.8807 (mtm) cc_final: 0.8276 (mtm) REVERT: A 1059 THR cc_start: 0.8461 (OUTLIER) cc_final: 0.8016 (p) outliers start: 17 outliers final: 10 residues processed: 92 average time/residue: 1.2085 time to fit residues: 120.7501 Evaluate side-chains 85 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 316 THR Chi-restraints excluded: chain A residue 445 VAL 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 1074 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 3 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 64 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 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 A1062 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.122792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.089220 restraints weight = 16611.411| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.21 r_work: 0.3142 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 10601 Z= 0.351 Angle : 0.593 11.597 14774 Z= 0.316 Chirality : 0.040 0.155 1677 Planarity : 0.004 0.035 1508 Dihedral : 21.082 179.914 2523 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % 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 (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: -0.41 (0.27), residues: 1009 helix: 1.22 (0.22), residues: 559 sheet: -1.28 (0.50), residues: 107 loop : -2.51 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 377 HIS 0.005 0.001 HIS A 711 PHE 0.023 0.002 PHE A1090 TYR 0.012 0.002 TYR A 135 ARG 0.007 0.001 ARG A 523 *********************** 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 98 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 1.118 Fit side-chains REVERT: A 228 ARG cc_start: 0.5114 (ppt170) cc_final: 0.4553 (ppt170) REVERT: A 273 PHE cc_start: 0.7607 (m-80) cc_final: 0.7402 (m-80) REVERT: A 412 GLN cc_start: 0.7857 (tp40) cc_final: 0.7469 (tm-30) REVERT: A 450 ASP cc_start: 0.7979 (m-30) cc_final: 0.7592 (m-30) REVERT: A 776 LYS cc_start: 0.8893 (tmtt) cc_final: 0.8538 (tmmm) REVERT: A 821 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8654 (tt) REVERT: A 870 VAL cc_start: 0.9112 (OUTLIER) cc_final: 0.8779 (m) REVERT: A 1059 THR cc_start: 0.8482 (OUTLIER) cc_final: 0.7933 (p) outliers start: 19 outliers final: 11 residues processed: 93 average time/residue: 1.1970 time to fit residues: 120.8667 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 : 1.052 ------------------------------------------------------------------------------- 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 1062 ASN 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: 9.9990 chunk 24 optimal weight: 9.9990 chunk 102 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 40 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 A1062 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.123043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.089530 restraints weight = 16558.587| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.21 r_work: 0.3148 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10601 Z= 0.320 Angle : 0.577 8.169 14774 Z= 0.310 Chirality : 0.039 0.149 1677 Planarity : 0.004 0.036 1508 Dihedral : 21.079 179.595 2523 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 2.30 % Allowed : 14.30 % 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: -0.48 (0.27), residues: 1009 helix: 1.17 (0.22), residues: 560 sheet: -1.32 (0.49), residues: 107 loop : -2.55 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 377 HIS 0.005 0.001 HIS A 527 PHE 0.028 0.002 PHE A 718 TYR 0.012 0.002 TYR A 646 ARG 0.007 0.001 ARG A 26 *********************** 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 96 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 1.047 Fit side-chains REVERT: A 228 ARG cc_start: 0.5135 (ppt170) cc_final: 0.4567 (ppt170) REVERT: A 273 PHE cc_start: 0.7711 (m-80) cc_final: 0.7508 (m-80) REVERT: A 386 LYS cc_start: 0.8280 (ttpp) cc_final: 0.7942 (mtmm) REVERT: A 412 GLN cc_start: 0.7847 (tp40) cc_final: 0.7477 (tm-30) REVERT: A 450 ASP cc_start: 0.7996 (m-30) cc_final: 0.7606 (m-30) REVERT: A 531 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8570 (mt) REVERT: A 776 LYS cc_start: 0.8931 (tmtt) cc_final: 0.8570 (tmmm) REVERT: A 821 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8661 (tt) REVERT: A 870 VAL cc_start: 0.9088 (OUTLIER) cc_final: 0.8767 (m) REVERT: A 913 MET cc_start: 0.8832 (mtm) cc_final: 0.8436 (mtp) REVERT: A 973 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8029 (mm-30) REVERT: A 1059 THR cc_start: 0.8509 (m) cc_final: 0.7931 (p) outliers start: 19 outliers final: 12 residues processed: 91 average time/residue: 1.1075 time to fit residues: 110.0169 Evaluate side-chains 92 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.963 ------------------------------------------------------------------------------- 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 531 LEU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 928 VAL Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1062 ASN 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: 6.9990 chunk 72 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 94 optimal weight: 50.0000 chunk 0 optimal weight: 8.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 = 0.3868 r_free = 0.3868 target = 0.126143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.092894 restraints weight = 16454.367| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.21 r_work: 0.3211 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2487 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= 0.181 Angle : 0.533 9.230 14774 Z= 0.287 Chirality : 0.036 0.144 1677 Planarity : 0.003 0.034 1508 Dihedral : 20.964 179.073 2523 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 1.94 % Allowed : 14.55 % Favored : 83.52 % 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: -0.25 (0.27), residues: 1009 helix: 1.38 (0.22), residues: 560 sheet: -1.06 (0.53), residues: 99 loop : -2.54 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 377 HIS 0.004 0.001 HIS A 366 PHE 0.027 0.001 PHE A 718 TYR 0.012 0.001 TYR A 646 ARG 0.008 0.000 ARG A 523 *********************** 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: 16 poor density : 81 time to evaluate : 1.022 Fit side-chains REVERT: A 228 ARG cc_start: 0.5042 (ppt170) cc_final: 0.4451 (ppt170) REVERT: A 386 LYS cc_start: 0.8302 (ttpp) cc_final: 0.7954 (mtmm) REVERT: A 412 GLN cc_start: 0.7803 (tp40) cc_final: 0.7388 (tm-30) REVERT: A 450 ASP cc_start: 0.8003 (m-30) cc_final: 0.7621 (m-30) REVERT: A 531 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8509 (mt) REVERT: A 693 LYS cc_start: 0.7673 (mtpt) cc_final: 0.7464 (pttt) REVERT: A 776 LYS cc_start: 0.8914 (tmtt) cc_final: 0.8561 (tptp) REVERT: A 870 VAL cc_start: 0.9007 (OUTLIER) cc_final: 0.8746 (m) REVERT: A 913 MET cc_start: 0.8826 (mtm) cc_final: 0.8433 (mtp) REVERT: A 973 GLU cc_start: 0.8464 (tt0) cc_final: 0.8032 (mm-30) REVERT: A 1059 THR cc_start: 0.8487 (OUTLIER) cc_final: 0.7949 (p) outliers start: 16 outliers final: 8 residues processed: 93 average time/residue: 1.1354 time to fit residues: 114.6666 Evaluate side-chains 87 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 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 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: 8.9990 chunk 48 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 103 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 22 optimal weight: 0.3980 chunk 23 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 A 765 GLN A1062 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.127823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.094856 restraints weight = 16551.843| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.22 r_work: 0.3244 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10601 Z= 0.171 Angle : 0.532 12.536 14774 Z= 0.283 Chirality : 0.036 0.174 1677 Planarity : 0.003 0.034 1508 Dihedral : 20.861 178.983 2523 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 1.33 % Allowed : 15.64 % Favored : 83.03 % 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: -0.15 (0.27), residues: 1009 helix: 1.46 (0.22), residues: 559 sheet: -1.13 (0.53), residues: 97 loop : -2.45 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 377 HIS 0.004 0.001 HIS A 366 PHE 0.023 0.001 PHE A 718 TYR 0.014 0.001 TYR A 646 ARG 0.008 0.000 ARG A 523 ********************** 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 97 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 1.021 Fit side-chains REVERT: A 228 ARG cc_start: 0.5129 (ppt170) cc_final: 0.4599 (ppt170) REVERT: A 386 LYS cc_start: 0.8301 (ttpp) cc_final: 0.7822 (mtmm) REVERT: A 412 GLN cc_start: 0.7776 (tp40) cc_final: 0.7372 (tm-30) REVERT: A 450 ASP cc_start: 0.8002 (m-30) cc_final: 0.7632 (m-30) REVERT: A 776 LYS cc_start: 0.8923 (tmtt) cc_final: 0.8580 (tptp) REVERT: A 870 VAL cc_start: 0.9001 (OUTLIER) cc_final: 0.8745 (m) REVERT: A 913 MET cc_start: 0.8813 (mtm) cc_final: 0.8159 (mtm) REVERT: A 973 GLU cc_start: 0.8460 (tt0) cc_final: 0.8048 (mm-30) REVERT: A 1059 THR cc_start: 0.8322 (m) cc_final: 0.7953 (p) outliers start: 11 outliers final: 8 residues processed: 94 average time/residue: 1.1825 time to fit residues: 120.9050 Evaluate side-chains 85 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 515 LYS Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 1062 ASN 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: 30.0000 chunk 88 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3872 r_free = 0.3872 target = 0.126389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.093088 restraints weight = 16520.812| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.21 r_work: 0.3216 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10601 Z= 0.221 Angle : 0.540 8.606 14774 Z= 0.290 Chirality : 0.037 0.146 1677 Planarity : 0.003 0.035 1508 Dihedral : 20.923 179.661 2523 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 1.70 % Allowed : 15.88 % Favored : 82.42 % 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: -0.10 (0.27), residues: 1009 helix: 1.48 (0.22), residues: 559 sheet: -1.09 (0.53), residues: 97 loop : -2.41 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 377 HIS 0.006 0.001 HIS A 527 PHE 0.023 0.002 PHE A 718 TYR 0.017 0.001 TYR A 646 ARG 0.008 0.000 ARG A 523 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6078.73 seconds wall clock time: 108 minutes 31.53 seconds (6511.53 seconds total)