Starting phenix.real_space_refine on Fri Jun 6 04:39:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7swq_25482/06_2025/7swq_25482.cif Found real_map, /net/cci-nas-00/data/ceres_data/7swq_25482/06_2025/7swq_25482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7swq_25482/06_2025/7swq_25482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7swq_25482/06_2025/7swq_25482.map" model { file = "/net/cci-nas-00/data/ceres_data/7swq_25482/06_2025/7swq_25482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7swq_25482/06_2025/7swq_25482.cif" } resolution = 3.79 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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 35 5.49 5 Mg 1 5.21 5 S 37 5.16 5 C 4310 2.51 5 N 1238 2.21 5 O 1377 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 6998 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 791, 6280 Classifications: {'peptide': 791} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 746} Chain breaks: 5 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 452 Classifications: {'RNA': 21} Modifications used: {'p5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 4, 'rna3p_pur': 10, 'rna3p_pyr': 5} Link IDs: {'rna2p': 6, 'rna3p': 14} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 265 Classifications: {'DNA': 1, 'RNA': 13} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 3, 'rna3p_pyr': 8} Link IDs: {'rna2p': 2, 'rna3p': 11} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A:plan': 1, ' U%rna2p_pyr:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.65, per 1000 atoms: 0.66 Number of scatterers: 6998 At special positions: 0 Unit cell: (83.72, 98.28, 111.93, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 37 16.00 P 35 15.00 Mg 1 11.99 O 1377 8.00 N 1238 7.00 C 4310 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: 1.85 Conformation dependent library (CDL) restraints added in 702.3 milliseconds 1558 Ramachandran restraints generated. 779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1494 Finding SS restraints... Warning! O6 atom is missing from residue G B 2 Was trying to link: C D 20 N4 with G B 2 O6, Saenger class: 19 Warning! O6 atom is missing from residue G B 2 Was trying to link: C D 20 N4 with G B 2 O6, Saenger class: 19 Secondary structure from input PDB file: 18 helices and 13 sheets defined 29.8% alpha, 11.1% beta 9 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 2.13 Creating SS restraints... Processing helix chain 'A' and resid 170 through 186 removed outlier: 3.580A pdb=" N ALA A 176 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 283 Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 357 through 369 Processing helix chain 'A' and resid 462 through 472 removed outlier: 3.914A pdb=" N VAL A 470 " --> pdb=" O ALA A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 490 removed outlier: 3.652A pdb=" N VAL A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 501 Processing helix chain 'A' and resid 565 through 583 removed outlier: 3.617A pdb=" N ARG A 570 " --> pdb=" O GLU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 618 removed outlier: 4.017A pdb=" N TYR A 611 " --> pdb=" O LEU A 607 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER A 614 " --> pdb=" O VAL A 610 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET A 615 " --> pdb=" O TYR A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 645 Processing helix chain 'A' and resid 657 through 662 removed outlier: 3.692A pdb=" N PHE A 662 " --> pdb=" O THR A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 680 removed outlier: 3.986A pdb=" N LEU A 674 " --> pdb=" O ALA A 670 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS A 675 " --> pdb=" O ASN A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 775 through 784 Processing helix chain 'A' and resid 801 through 821 removed outlier: 3.627A pdb=" N VAL A 805 " --> pdb=" O GLN A 801 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU A 810 " --> pdb=" O LEU A 806 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE A 813 " --> pdb=" O GLU A 809 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA A 818 " --> pdb=" O ARG A 814 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER A 819 " --> pdb=" O LYS A 815 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 820 " --> pdb=" O ALA A 816 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLU A 821 " --> pdb=" O CYS A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 915 removed outlier: 3.528A pdb=" N GLN A 908 " --> pdb=" O ALA A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 945 removed outlier: 4.089A pdb=" N ALA A 934 " --> pdb=" O PRO A 930 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N HIS A 935 " --> pdb=" O ALA A 931 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE A 939 " --> pdb=" O HIS A 935 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA A 941 " --> pdb=" O ALA A 937 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ARG A 942 " --> pdb=" O ALA A 938 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N PHE A 943 " --> pdb=" O PHE A 939 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TYR A 944 " --> pdb=" O ARG A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 982 removed outlier: 3.733A pdb=" N LYS A 982 " --> pdb=" O GLU A 979 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 139 through 140 Processing sheet with id=AA2, first strand: chain 'A' and resid 509 through 511 Processing sheet with id=AA3, first strand: chain 'A' and resid 150 through 151 removed outlier: 3.656A pdb=" N ASN A 503 " --> pdb=" O ASP A 151 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 196 through 197 removed outlier: 3.885A pdb=" N LYS A 242 " --> pdb=" O ASP A 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 305 through 306 Processing sheet with id=AA6, first strand: chain 'A' and resid 309 through 311 Processing sheet with id=AA7, first strand: chain 'A' and resid 315 through 316 Processing sheet with id=AA8, first strand: chain 'A' and resid 439 through 440 removed outlier: 3.897A pdb=" N SER A 440 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLN A 432 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ARG A 386 " --> pdb=" O GLY A 434 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 531 through 532 removed outlier: 4.132A pdb=" N VAL A 686 " --> pdb=" O LYS A 522 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 556 through 559 Processing sheet with id=AB2, first strand: chain 'A' and resid 703 through 705 removed outlier: 6.424A pdb=" N ILE A 704 " --> pdb=" O ILE A 791 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 708 through 710 Processing sheet with id=AB4, first strand: chain 'A' and resid 829 through 834 removed outlier: 6.749A pdb=" N PHE A 830 " --> pdb=" O LEU A 896 " (cutoff:3.500A) 195 hydrogen bonds defined for protein. 549 hydrogen bond angles defined for protein. NA hbond rejected because one of the atoms is absent Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 2.43 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1875 1.33 - 1.45: 1351 1.45 - 1.57: 3867 1.57 - 1.69: 67 1.69 - 1.81: 52 Bond restraints: 7212 Sorted by residual: bond pdb=" CA GLY A 434 " pdb=" C GLY A 434 " ideal model delta sigma weight residual 1.530 1.514 0.017 1.04e-02 9.25e+03 2.56e+00 bond pdb=" CB VAL A 928 " pdb=" CG2 VAL A 928 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.46e+00 bond pdb=" N GLY A 434 " pdb=" CA GLY A 434 " ideal model delta sigma weight residual 1.464 1.448 0.016 1.12e-02 7.97e+03 2.15e+00 bond pdb=" C TRP A 732 " pdb=" N PRO A 733 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.23e-02 6.61e+03 2.12e+00 bond pdb=" C LEU A 533 " pdb=" N PRO A 534 " ideal model delta sigma weight residual 1.332 1.316 0.016 1.12e-02 7.97e+03 2.01e+00 ... (remaining 7207 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 9282 1.36 - 2.73: 514 2.73 - 4.09: 91 4.09 - 5.46: 23 5.46 - 6.82: 7 Bond angle restraints: 9917 Sorted by residual: angle pdb=" C THR A 866 " pdb=" N LYS A 867 " pdb=" CA LYS A 867 " ideal model delta sigma weight residual 121.54 128.36 -6.82 1.91e+00 2.74e-01 1.27e+01 angle pdb=" C3' A B 12 " pdb=" O3' A B 12 " pdb=" P A B 13 " ideal model delta sigma weight residual 120.20 125.55 -5.35 1.50e+00 4.44e-01 1.27e+01 angle pdb=" C GLY A 191 " pdb=" N ARG A 192 " pdb=" CA ARG A 192 " ideal model delta sigma weight residual 121.54 128.21 -6.67 1.91e+00 2.74e-01 1.22e+01 angle pdb=" N LEU A 252 " pdb=" CA LEU A 252 " pdb=" C LEU A 252 " ideal model delta sigma weight residual 114.31 110.02 4.29 1.29e+00 6.01e-01 1.11e+01 angle pdb=" O3' A B 12 " pdb=" C3' A B 12 " pdb=" C2' A B 12 " ideal model delta sigma weight residual 109.50 114.18 -4.68 1.50e+00 4.44e-01 9.73e+00 ... (remaining 9912 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 4260 35.94 - 71.89: 144 71.89 - 107.83: 22 107.83 - 143.77: 0 143.77 - 179.72: 4 Dihedral angle restraints: 4430 sinusoidal: 2121 harmonic: 2309 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 52.28 179.72 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA GLU A 461 " pdb=" C GLU A 461 " pdb=" N LYS A 462 " pdb=" CA LYS A 462 " ideal model delta harmonic sigma weight residual 180.00 159.65 20.35 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" C4' C D 20 " pdb=" C3' C D 20 " pdb=" O3' C D 20 " pdb=" P A D 21 " ideal model delta sinusoidal sigma weight residual 220.00 42.27 177.73 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 4427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 875 0.049 - 0.099: 223 0.099 - 0.148: 38 0.148 - 0.197: 2 0.197 - 0.247: 1 Chirality restraints: 1139 Sorted by residual: chirality pdb=" CB ILE A 927 " pdb=" CA ILE A 927 " pdb=" CG1 ILE A 927 " pdb=" CG2 ILE A 927 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" C3' A B 12 " pdb=" C4' A B 12 " pdb=" O3' A B 12 " pdb=" C2' A B 12 " both_signs ideal model delta sigma weight residual False -2.74 -2.55 -0.19 2.00e-01 2.50e+01 9.41e-01 chirality pdb=" CB VAL A 678 " pdb=" CA VAL A 678 " pdb=" CG1 VAL A 678 " pdb=" CG2 VAL A 678 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.15 2.00e-01 2.50e+01 6.00e-01 ... (remaining 1136 not shown) Planarity restraints: 1150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 732 " 0.014 2.00e-02 2.50e+03 1.19e-02 3.55e+00 pdb=" CG TRP A 732 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP A 732 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 732 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 732 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 732 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 732 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 732 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 732 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 732 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 300 " 0.139 9.50e-02 1.11e+02 6.28e-02 3.09e+00 pdb=" NE ARG A 300 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 300 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 300 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 300 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 929 " 0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO A 930 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 930 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 930 " 0.022 5.00e-02 4.00e+02 ... (remaining 1147 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 55 2.51 - 3.11: 5007 3.11 - 3.71: 10739 3.71 - 4.30: 14223 4.30 - 4.90: 23998 Nonbonded interactions: 54022 Sorted by model distance: nonbonded pdb=" OD2 ASP A 709 " pdb="MG MG A1001 " model vdw 1.915 2.170 nonbonded pdb=" ND1 HIS A 935 " pdb="MG MG A1001 " model vdw 2.071 2.250 nonbonded pdb=" O2' C D 20 " pdb=" OP1 A D 21 " model vdw 2.186 3.040 nonbonded pdb=" NH2 ARG A 940 " pdb=" OH TYR A 944 " model vdw 2.200 3.120 nonbonded pdb=" NH2 ARG A 920 " pdb=" OP1 G B 3 " model vdw 2.202 3.120 ... (remaining 54017 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 group one per residue 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: 0.460 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.110 Find NCS groups from input model: 0.080 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: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 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 7212 Z= 0.205 Angle : 0.736 6.819 9917 Z= 0.419 Chirality : 0.043 0.247 1139 Planarity : 0.005 0.063 1150 Dihedral : 18.242 179.716 2936 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -2.38 (0.29), residues: 779 helix: -0.54 (0.36), residues: 212 sheet: -1.58 (0.50), residues: 118 loop : -2.17 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 732 HIS 0.005 0.001 HIS A 892 PHE 0.025 0.002 PHE A 874 TYR 0.021 0.002 TYR A 638 ARG 0.014 0.001 ARG A 300 Details of bonding type rmsd hydrogen bonds : bond 0.17742 ( 217) hydrogen bonds : angle 7.30096 ( 593) covalent geometry : bond 0.00448 ( 7212) covalent geometry : angle 0.73631 ( 9917) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1558 Ramachandran restraints generated. 779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1558 Ramachandran restraints generated. 779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 MET cc_start: 0.4031 (mmp) cc_final: 0.3444 (mmp) REVERT: A 567 ASN cc_start: 0.7178 (t0) cc_final: 0.6943 (t0) REVERT: A 912 ASN cc_start: 0.8469 (t0) cc_final: 0.8172 (t0) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.2149 time to fit residues: 36.4650 Evaluate side-chains 82 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 7.9990 chunk 62 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 64 optimal weight: 0.0170 chunk 24 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 overall best weight: 1.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 GLN A 602 GLN A 609 HIS ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.123364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.090823 restraints weight = 15979.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.093649 restraints weight = 8085.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.095388 restraints weight = 5284.700| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7212 Z= 0.134 Angle : 0.631 8.313 9917 Z= 0.323 Chirality : 0.043 0.187 1139 Planarity : 0.004 0.037 1150 Dihedral : 17.799 179.123 1382 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 1.45 % Allowed : 11.16 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -2.08 (0.29), residues: 779 helix: 0.09 (0.37), residues: 214 sheet: -1.41 (0.47), residues: 131 loop : -2.21 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 759 HIS 0.007 0.001 HIS A 609 PHE 0.013 0.001 PHE A 874 TYR 0.017 0.001 TYR A 932 ARG 0.008 0.001 ARG A 361 Details of bonding type rmsd hydrogen bonds : bond 0.03397 ( 217) hydrogen bonds : angle 5.45908 ( 593) covalent geometry : bond 0.00301 ( 7212) covalent geometry : angle 0.63123 ( 9917) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1558 Ramachandran restraints generated. 779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1558 Ramachandran restraints generated. 779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 277 GLU cc_start: 0.8557 (tt0) cc_final: 0.7671 (tt0) REVERT: A 345 GLN cc_start: 0.9595 (pt0) cc_final: 0.8919 (pp30) REVERT: A 444 MET cc_start: 0.6274 (mmp) cc_final: 0.5564 (mmp) REVERT: A 567 ASN cc_start: 0.8020 (t0) cc_final: 0.7780 (t0) REVERT: A 575 GLU cc_start: 0.8711 (tp30) cc_final: 0.8431 (tp30) outliers start: 10 outliers final: 8 residues processed: 106 average time/residue: 0.2156 time to fit residues: 30.2605 Evaluate side-chains 91 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 655 CYS Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 869 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 32 optimal weight: 0.0770 chunk 64 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 14 optimal weight: 0.5980 chunk 70 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 26 optimal weight: 30.0000 chunk 68 optimal weight: 2.9990 overall best weight: 2.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 671 ASN ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.120917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.088875 restraints weight = 16461.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.091579 restraints weight = 8419.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.093268 restraints weight = 5557.323| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7212 Z= 0.171 Angle : 0.630 7.371 9917 Z= 0.327 Chirality : 0.044 0.189 1139 Planarity : 0.004 0.038 1150 Dihedral : 17.749 178.116 1382 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 2.61 % Allowed : 14.35 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -2.03 (0.29), residues: 779 helix: 0.10 (0.37), residues: 215 sheet: -1.30 (0.48), residues: 132 loop : -2.19 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 213 HIS 0.002 0.001 HIS A 837 PHE 0.015 0.001 PHE A 874 TYR 0.026 0.002 TYR A 197 ARG 0.004 0.000 ARG A 361 Details of bonding type rmsd hydrogen bonds : bond 0.03553 ( 217) hydrogen bonds : angle 5.35523 ( 593) covalent geometry : bond 0.00384 ( 7212) covalent geometry : angle 0.63044 ( 9917) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1558 Ramachandran restraints generated. 779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1558 Ramachandran restraints generated. 779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 ILE cc_start: 0.8283 (OUTLIER) cc_final: 0.8070 (mm) REVERT: A 213 TRP cc_start: 0.8287 (t60) cc_final: 0.8052 (t60) REVERT: A 337 LEU cc_start: 0.7688 (tp) cc_final: 0.7369 (tp) REVERT: A 341 GLU cc_start: 0.8255 (pm20) cc_final: 0.7989 (pm20) REVERT: A 444 MET cc_start: 0.6332 (mmp) cc_final: 0.5731 (mmp) REVERT: A 506 GLU cc_start: 0.8742 (tp30) cc_final: 0.8475 (tp30) REVERT: A 550 MET cc_start: 0.8158 (mmm) cc_final: 0.7713 (mmm) REVERT: A 575 GLU cc_start: 0.8657 (tp30) cc_final: 0.8308 (tp30) REVERT: A 793 TYR cc_start: 0.8677 (OUTLIER) cc_final: 0.8228 (t80) outliers start: 18 outliers final: 10 residues processed: 97 average time/residue: 0.1869 time to fit residues: 24.6553 Evaluate side-chains 89 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 655 CYS Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 793 TYR Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 869 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.119124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.086219 restraints weight = 16430.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.088958 restraints weight = 8350.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.090694 restraints weight = 5518.673| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7212 Z= 0.190 Angle : 0.631 7.695 9917 Z= 0.328 Chirality : 0.044 0.188 1139 Planarity : 0.004 0.037 1150 Dihedral : 17.728 178.097 1382 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer: Outliers : 2.46 % Allowed : 17.68 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -2.00 (0.29), residues: 779 helix: 0.17 (0.37), residues: 216 sheet: -1.31 (0.48), residues: 134 loop : -2.20 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 213 HIS 0.002 0.001 HIS A 488 PHE 0.016 0.002 PHE A 874 TYR 0.015 0.002 TYR A 204 ARG 0.004 0.000 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.03539 ( 217) hydrogen bonds : angle 5.29592 ( 593) covalent geometry : bond 0.00431 ( 7212) covalent geometry : angle 0.63055 ( 9917) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1558 Ramachandran restraints generated. 779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1558 Ramachandran restraints generated. 779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8078 (tm-30) REVERT: A 337 LEU cc_start: 0.7743 (tp) cc_final: 0.7407 (tp) REVERT: A 341 GLU cc_start: 0.8324 (pm20) cc_final: 0.8044 (pm20) REVERT: A 444 MET cc_start: 0.6462 (mmp) cc_final: 0.5912 (mmp) REVERT: A 506 GLU cc_start: 0.8746 (tp30) cc_final: 0.8484 (tp30) REVERT: A 550 MET cc_start: 0.8216 (mmm) cc_final: 0.7790 (mmm) REVERT: A 575 GLU cc_start: 0.8619 (tp30) cc_final: 0.8329 (tp30) REVERT: A 771 MET cc_start: 0.7672 (mtm) cc_final: 0.7071 (mtm) REVERT: A 793 TYR cc_start: 0.8717 (OUTLIER) cc_final: 0.8078 (t80) REVERT: A 920 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8796 (mtm180) outliers start: 17 outliers final: 14 residues processed: 90 average time/residue: 0.1964 time to fit residues: 23.8645 Evaluate side-chains 87 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 655 CYS Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 793 TYR Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 869 CYS Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 974 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 32 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 80 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.116509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.084242 restraints weight = 16618.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.086807 restraints weight = 8679.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.088430 restraints weight = 5858.213| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 7212 Z= 0.287 Angle : 0.717 8.553 9917 Z= 0.374 Chirality : 0.047 0.186 1139 Planarity : 0.005 0.042 1150 Dihedral : 17.888 177.696 1382 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.40 % Favored : 89.60 % Rotamer: Outliers : 4.49 % Allowed : 17.25 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -2.24 (0.29), residues: 779 helix: -0.13 (0.36), residues: 217 sheet: -0.96 (0.52), residues: 108 loop : -2.43 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 213 HIS 0.003 0.001 HIS A 837 PHE 0.020 0.002 PHE A 874 TYR 0.032 0.002 TYR A 197 ARG 0.004 0.000 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.04264 ( 217) hydrogen bonds : angle 5.57164 ( 593) covalent geometry : bond 0.00644 ( 7212) covalent geometry : angle 0.71707 ( 9917) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1558 Ramachandran restraints generated. 779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1558 Ramachandran restraints generated. 779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 67 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 337 LEU cc_start: 0.7748 (tp) cc_final: 0.7350 (tp) REVERT: A 341 GLU cc_start: 0.8378 (pm20) cc_final: 0.8130 (pm20) REVERT: A 444 MET cc_start: 0.6480 (mmp) cc_final: 0.6195 (mmp) REVERT: A 550 MET cc_start: 0.8244 (mmm) cc_final: 0.7803 (mmm) REVERT: A 575 GLU cc_start: 0.8713 (tp30) cc_final: 0.8490 (tp30) REVERT: A 793 TYR cc_start: 0.8716 (OUTLIER) cc_final: 0.7996 (t80) REVERT: A 838 HIS cc_start: 0.8296 (OUTLIER) cc_final: 0.7766 (p90) REVERT: A 896 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8787 (mm) REVERT: A 920 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.8714 (mtm180) outliers start: 31 outliers final: 19 residues processed: 95 average time/residue: 0.1915 time to fit residues: 24.7385 Evaluate side-chains 85 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 62 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 655 CYS Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 793 TYR Chi-restraints excluded: chain A residue 805 VAL Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 838 HIS Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 869 CYS Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 920 ARG Chi-restraints excluded: chain A residue 974 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 65 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 671 ASN ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.119347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.087402 restraints weight = 16479.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.090084 restraints weight = 8432.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.091791 restraints weight = 5600.203| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7212 Z= 0.149 Angle : 0.630 8.105 9917 Z= 0.327 Chirality : 0.043 0.185 1139 Planarity : 0.004 0.036 1150 Dihedral : 17.807 179.978 1382 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 4.64 % Allowed : 19.13 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -2.14 (0.29), residues: 779 helix: 0.23 (0.38), residues: 212 sheet: -1.57 (0.45), residues: 142 loop : -2.31 (0.26), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 213 HIS 0.002 0.001 HIS A 892 PHE 0.014 0.001 PHE A 902 TYR 0.023 0.002 TYR A 197 ARG 0.005 0.000 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.03364 ( 217) hydrogen bonds : angle 5.22957 ( 593) covalent geometry : bond 0.00340 ( 7212) covalent geometry : angle 0.63006 ( 9917) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1558 Ramachandran restraints generated. 779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1558 Ramachandran restraints generated. 779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 78 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8026 (tm-30) REVERT: A 432 GLN cc_start: 0.6920 (OUTLIER) cc_final: 0.6372 (mp10) REVERT: A 500 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.8059 (t80) REVERT: A 506 GLU cc_start: 0.8726 (tp30) cc_final: 0.8478 (tp30) REVERT: A 550 MET cc_start: 0.8176 (mmm) cc_final: 0.7758 (mmm) REVERT: A 575 GLU cc_start: 0.8671 (tp30) cc_final: 0.8435 (tp30) REVERT: A 732 TRP cc_start: 0.7135 (t-100) cc_final: 0.6600 (t-100) REVERT: A 793 TYR cc_start: 0.8700 (OUTLIER) cc_final: 0.7981 (t80) REVERT: A 896 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8734 (mm) REVERT: A 932 TYR cc_start: 0.8520 (OUTLIER) cc_final: 0.8027 (t80) outliers start: 32 outliers final: 18 residues processed: 106 average time/residue: 0.2007 time to fit residues: 28.6270 Evaluate side-chains 92 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 432 GLN Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 500 PHE Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 655 CYS Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 793 TYR Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 869 CYS Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 932 TYR Chi-restraints excluded: chain A residue 974 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 20.0000 chunk 34 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 671 ASN ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.121275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.088348 restraints weight = 16928.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.091235 restraints weight = 8237.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.093027 restraints weight = 5340.509| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7212 Z= 0.161 Angle : 0.640 8.276 9917 Z= 0.329 Chirality : 0.043 0.185 1139 Planarity : 0.004 0.037 1150 Dihedral : 17.796 179.870 1382 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 4.35 % Allowed : 20.72 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -2.08 (0.29), residues: 779 helix: 0.30 (0.38), residues: 212 sheet: -1.59 (0.45), residues: 142 loop : -2.27 (0.27), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 213 HIS 0.002 0.001 HIS A 892 PHE 0.011 0.001 PHE A 874 TYR 0.020 0.002 TYR A 197 ARG 0.004 0.000 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.03385 ( 217) hydrogen bonds : angle 5.14777 ( 593) covalent geometry : bond 0.00367 ( 7212) covalent geometry : angle 0.63976 ( 9917) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1558 Ramachandran restraints generated. 779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1558 Ramachandran restraints generated. 779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 72 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 432 GLN cc_start: 0.6896 (OUTLIER) cc_final: 0.6267 (mp10) REVERT: A 500 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.8078 (t80) REVERT: A 506 GLU cc_start: 0.8751 (tp30) cc_final: 0.8512 (tp30) REVERT: A 550 MET cc_start: 0.8163 (mmm) cc_final: 0.7744 (mmm) REVERT: A 575 GLU cc_start: 0.8652 (tp30) cc_final: 0.8431 (tp30) REVERT: A 732 TRP cc_start: 0.7177 (t-100) cc_final: 0.6872 (t-100) REVERT: A 793 TYR cc_start: 0.8668 (OUTLIER) cc_final: 0.7935 (t80) REVERT: A 896 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8699 (mm) REVERT: A 927 ILE cc_start: 0.8338 (mt) cc_final: 0.7995 (mt) REVERT: A 932 TYR cc_start: 0.8567 (OUTLIER) cc_final: 0.7940 (t80) outliers start: 30 outliers final: 19 residues processed: 98 average time/residue: 0.1665 time to fit residues: 22.8992 Evaluate side-chains 93 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 432 GLN Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 500 PHE Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 655 CYS Chi-restraints excluded: chain A residue 671 ASN Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 793 TYR Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 869 CYS Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 932 TYR Chi-restraints excluded: chain A residue 974 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 12 optimal weight: 6.9990 chunk 65 optimal weight: 0.0980 chunk 10 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 80 optimal weight: 30.0000 chunk 14 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.113730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.081588 restraints weight = 16069.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.084193 restraints weight = 8068.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.085829 restraints weight = 5250.772| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 7212 Z= 0.241 Angle : 0.693 8.605 9917 Z= 0.358 Chirality : 0.046 0.185 1139 Planarity : 0.004 0.039 1150 Dihedral : 17.868 179.754 1382 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Rotamer: Outliers : 4.35 % Allowed : 21.16 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -2.27 (0.29), residues: 779 helix: 0.09 (0.37), residues: 217 sheet: -1.70 (0.45), residues: 142 loop : -2.38 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 213 HIS 0.003 0.001 HIS A 894 PHE 0.015 0.002 PHE A 874 TYR 0.017 0.002 TYR A 197 ARG 0.005 0.000 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.03971 ( 217) hydrogen bonds : angle 5.27769 ( 593) covalent geometry : bond 0.00545 ( 7212) covalent geometry : angle 0.69348 ( 9917) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1558 Ramachandran restraints generated. 779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1558 Ramachandran restraints generated. 779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 66 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 432 GLN cc_start: 0.7077 (OUTLIER) cc_final: 0.6547 (mp10) REVERT: A 500 PHE cc_start: 0.8499 (OUTLIER) cc_final: 0.8139 (t80) REVERT: A 550 MET cc_start: 0.8341 (mmm) cc_final: 0.7840 (mmm) REVERT: A 575 GLU cc_start: 0.8800 (tp30) cc_final: 0.8569 (tp30) REVERT: A 623 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8580 (mm) REVERT: A 732 TRP cc_start: 0.7596 (t-100) cc_final: 0.7273 (t-100) REVERT: A 793 TYR cc_start: 0.8801 (OUTLIER) cc_final: 0.7944 (t80) REVERT: A 896 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8774 (mm) REVERT: A 932 TYR cc_start: 0.8663 (OUTLIER) cc_final: 0.8054 (t80) outliers start: 30 outliers final: 19 residues processed: 92 average time/residue: 0.1759 time to fit residues: 22.8648 Evaluate side-chains 88 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 63 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 432 GLN Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 500 PHE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 655 CYS Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 793 TYR Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 869 CYS Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 932 TYR Chi-restraints excluded: chain A residue 974 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 0.0070 chunk 32 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 overall best weight: 1.7604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 GLN A 671 ASN ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.118474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.085310 restraints weight = 16437.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.088035 restraints weight = 8252.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.089723 restraints weight = 5393.055| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7212 Z= 0.145 Angle : 0.653 9.124 9917 Z= 0.331 Chirality : 0.043 0.185 1139 Planarity : 0.004 0.040 1150 Dihedral : 17.779 178.571 1382 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 4.06 % Allowed : 21.88 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -2.15 (0.29), residues: 779 helix: 0.22 (0.37), residues: 218 sheet: -1.67 (0.42), residues: 157 loop : -2.32 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 213 HIS 0.002 0.001 HIS A 892 PHE 0.010 0.001 PHE A 874 TYR 0.018 0.001 TYR A 197 ARG 0.005 0.000 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.03361 ( 217) hydrogen bonds : angle 5.08189 ( 593) covalent geometry : bond 0.00336 ( 7212) covalent geometry : angle 0.65282 ( 9917) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1558 Ramachandran restraints generated. 779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1558 Ramachandran restraints generated. 779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 74 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8119 (tm-30) REVERT: A 432 GLN cc_start: 0.7229 (OUTLIER) cc_final: 0.6661 (mp10) REVERT: A 500 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.8014 (t80) REVERT: A 550 MET cc_start: 0.8207 (mmm) cc_final: 0.7751 (mmm) REVERT: A 575 GLU cc_start: 0.8687 (tp30) cc_final: 0.8478 (tp30) REVERT: A 732 TRP cc_start: 0.7225 (t-100) cc_final: 0.6948 (t-100) REVERT: A 793 TYR cc_start: 0.8716 (OUTLIER) cc_final: 0.7942 (t80) REVERT: A 896 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8718 (mm) REVERT: A 927 ILE cc_start: 0.8403 (mt) cc_final: 0.8073 (mt) REVERT: A 932 TYR cc_start: 0.8551 (OUTLIER) cc_final: 0.7909 (t80) outliers start: 28 outliers final: 17 residues processed: 98 average time/residue: 0.1663 time to fit residues: 22.9496 Evaluate side-chains 92 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 432 GLN Chi-restraints excluded: chain A residue 500 PHE Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 655 CYS Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 793 TYR Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 869 CYS Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 932 TYR Chi-restraints excluded: chain A residue 974 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 62 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN ** A 894 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.122077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.090281 restraints weight = 16474.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.093084 restraints weight = 8228.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.094831 restraints weight = 5361.949| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7212 Z= 0.121 Angle : 0.654 10.254 9917 Z= 0.327 Chirality : 0.042 0.185 1139 Planarity : 0.004 0.059 1150 Dihedral : 17.706 177.732 1382 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 3.77 % Allowed : 22.75 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -1.93 (0.30), residues: 779 helix: 0.41 (0.37), residues: 217 sheet: -1.34 (0.44), residues: 150 loop : -2.27 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 213 HIS 0.002 0.000 HIS A 892 PHE 0.010 0.001 PHE A 148 TYR 0.017 0.001 TYR A 197 ARG 0.007 0.000 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.03101 ( 217) hydrogen bonds : angle 4.98834 ( 593) covalent geometry : bond 0.00278 ( 7212) covalent geometry : angle 0.65406 ( 9917) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1558 Ramachandran restraints generated. 779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1558 Ramachandran restraints generated. 779 Oldfield, 0 Emsley, 779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8163 (tm-30) REVERT: A 432 GLN cc_start: 0.7066 (OUTLIER) cc_final: 0.6463 (mp10) REVERT: A 500 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.7931 (t80) REVERT: A 506 GLU cc_start: 0.8892 (tp30) cc_final: 0.8661 (tp30) REVERT: A 550 MET cc_start: 0.8128 (mmm) cc_final: 0.7696 (mmm) REVERT: A 579 MET cc_start: 0.8178 (tpp) cc_final: 0.7781 (tpp) REVERT: A 732 TRP cc_start: 0.7032 (t-100) cc_final: 0.6751 (t-100) REVERT: A 932 TYR cc_start: 0.8426 (OUTLIER) cc_final: 0.7750 (t80) outliers start: 26 outliers final: 19 residues processed: 95 average time/residue: 0.1964 time to fit residues: 26.5468 Evaluate side-chains 95 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 432 GLN Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 500 PHE Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 655 CYS Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 793 TYR Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 869 CYS Chi-restraints excluded: chain A residue 907 ILE Chi-restraints excluded: chain A residue 932 TYR Chi-restraints excluded: chain A residue 974 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 81 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 14 optimal weight: 0.4980 chunk 1 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.120412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.087389 restraints weight = 16473.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.090140 restraints weight = 8205.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.091886 restraints weight = 5348.164| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7212 Z= 0.135 Angle : 0.657 9.992 9917 Z= 0.330 Chirality : 0.042 0.184 1139 Planarity : 0.004 0.039 1150 Dihedral : 17.671 178.610 1382 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 3.77 % Allowed : 22.75 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % 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: -1.90 (0.30), residues: 779 helix: 0.43 (0.37), residues: 216 sheet: -1.34 (0.45), residues: 148 loop : -2.23 (0.27), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 213 HIS 0.002 0.000 HIS A 251 PHE 0.010 0.001 PHE A 243 TYR 0.016 0.001 TYR A 197 ARG 0.002 0.000 ARG A 942 Details of bonding type rmsd hydrogen bonds : bond 0.03194 ( 217) hydrogen bonds : angle 4.96605 ( 593) covalent geometry : bond 0.00315 ( 7212) covalent geometry : angle 0.65655 ( 9917) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2302.97 seconds wall clock time: 40 minutes 51.27 seconds (2451.27 seconds total)