Starting phenix.real_space_refine on Wed Feb 12 03:58:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7swq_25482/02_2025/7swq_25482.cif Found real_map, /net/cci-nas-00/data/ceres_data/7swq_25482/02_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_25482/02_2025/7swq_25482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7swq_25482/02_2025/7swq_25482.map" model { file = "/net/cci-nas-00/data/ceres_data/7swq_25482/02_2025/7swq_25482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7swq_25482/02_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-5592/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: 1.80 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 2.30 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: 2.59 Time building geometry restraints manager: 2.11 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: 0.780 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.240 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.740 ------------------------------------------------------------------------------- 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= 0.285 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 *********************** 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 : 1.093 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: 0.2489 time to fit residues: 42.4396 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 : 0.822 ------------------------------------------------------------------------------- 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 = 42)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.090810 restraints weight = 15979.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.093635 restraints weight = 8093.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.095426 restraints weight = 5289.862| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 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= 0.190 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 *********************** 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 : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 277 GLU cc_start: 0.8555 (tt0) cc_final: 0.7677 (tt0) REVERT: A 345 GLN cc_start: 0.9593 (pt0) cc_final: 0.8917 (pp30) REVERT: A 444 MET cc_start: 0.6262 (mmp) cc_final: 0.5549 (mmp) REVERT: A 567 ASN cc_start: 0.8019 (t0) cc_final: 0.7780 (t0) REVERT: A 575 GLU cc_start: 0.8711 (tp30) cc_final: 0.8432 (tp30) outliers start: 10 outliers final: 8 residues processed: 106 average time/residue: 0.2082 time to fit residues: 29.0902 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 : 0.784 ------------------------------------------------------------------------------- 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: 0.0980 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: 0.3980 chunk 70 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 26 optimal weight: 30.0000 chunk 68 optimal weight: 3.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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 = 0.3894 r_free = 0.3894 target = 0.120278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.088185 restraints weight = 16430.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.090946 restraints weight = 8259.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.092712 restraints weight = 5398.743| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2421 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= 0.259 Angle : 0.641 7.510 9917 Z= 0.333 Chirality : 0.044 0.189 1139 Planarity : 0.004 0.038 1150 Dihedral : 17.758 177.890 1382 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 2.75 % Allowed : 14.49 % Favored : 82.75 % 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: -2.05 (0.29), residues: 779 helix: 0.06 (0.37), residues: 215 sheet: -1.31 (0.48), residues: 132 loop : -2.20 (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 0.016 0.002 PHE A 874 TYR 0.028 0.002 TYR A 197 ARG 0.004 0.000 ARG A 361 *********************** 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 101 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.8049 (mm) REVERT: A 197 TYR cc_start: 0.8188 (t80) cc_final: 0.7967 (t80) REVERT: A 213 TRP cc_start: 0.8292 (t60) cc_final: 0.8009 (t60) REVERT: A 337 LEU cc_start: 0.7708 (tp) cc_final: 0.7296 (tp) REVERT: A 341 GLU cc_start: 0.8308 (pm20) cc_final: 0.7962 (pm20) REVERT: A 442 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8446 (pp) REVERT: A 444 MET cc_start: 0.6383 (mmp) cc_final: 0.5790 (mmp) REVERT: A 506 GLU cc_start: 0.8768 (tp30) cc_final: 0.8548 (tp30) REVERT: A 550 MET cc_start: 0.8148 (mmm) cc_final: 0.7688 (mmm) REVERT: A 567 ASN cc_start: 0.8042 (t0) cc_final: 0.7840 (t0) REVERT: A 575 GLU cc_start: 0.8658 (tp30) cc_final: 0.8312 (tp30) REVERT: A 793 TYR cc_start: 0.8681 (OUTLIER) cc_final: 0.8093 (t80) outliers start: 19 outliers final: 10 residues processed: 96 average time/residue: 0.2038 time to fit residues: 26.2858 Evaluate side-chains 86 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.768 ------------------------------------------------------------------------------- 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 442 LEU 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: 1.9990 chunk 19 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 = 0.3871 r_free = 0.3871 target = 0.118633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.086433 restraints weight = 16732.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.089092 restraints weight = 8573.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.090742 restraints weight = 5696.246| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7212 Z= 0.303 Angle : 0.649 7.942 9917 Z= 0.338 Chirality : 0.044 0.187 1139 Planarity : 0.004 0.037 1150 Dihedral : 17.768 177.986 1382 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.01 % Favored : 89.99 % Rotamer: Outliers : 2.90 % Allowed : 17.10 % Favored : 80.00 % 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: -2.06 (0.29), residues: 779 helix: 0.13 (0.37), residues: 216 sheet: -1.37 (0.48), residues: 133 loop : -2.24 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 732 HIS 0.003 0.001 HIS A 894 PHE 0.017 0.002 PHE A 874 TYR 0.016 0.002 TYR A 204 ARG 0.004 0.000 ARG A 599 *********************** 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 97 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 TYR cc_start: 0.8118 (t80) cc_final: 0.7820 (t80) REVERT: A 208 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8063 (tm-30) REVERT: A 337 LEU cc_start: 0.7753 (tp) cc_final: 0.7316 (tp) REVERT: A 341 GLU cc_start: 0.8333 (pm20) cc_final: 0.7961 (pm20) REVERT: A 444 MET cc_start: 0.6465 (mmp) cc_final: 0.6007 (mmp) REVERT: A 550 MET cc_start: 0.8202 (mmm) cc_final: 0.7787 (mmm) REVERT: A 575 GLU cc_start: 0.8647 (tp30) cc_final: 0.8335 (tp30) REVERT: A 793 TYR cc_start: 0.8719 (OUTLIER) cc_final: 0.8114 (t80) REVERT: A 920 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.8783 (mtm180) outliers start: 20 outliers final: 14 residues processed: 94 average time/residue: 0.1995 time to fit residues: 25.2389 Evaluate side-chains 88 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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: 1.9990 chunk 64 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 0.7980 chunk 29 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 30.0000 chunk 80 optimal weight: 30.0000 chunk 44 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3917 r_free = 0.3917 target = 0.121773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.090166 restraints weight = 16262.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.092990 restraints weight = 8092.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.094808 restraints weight = 5253.465| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7212 Z= 0.173 Angle : 0.585 7.440 9917 Z= 0.301 Chirality : 0.042 0.187 1139 Planarity : 0.004 0.037 1150 Dihedral : 17.641 179.686 1382 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 3.91 % Allowed : 17.83 % 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: -1.91 (0.30), residues: 779 helix: 0.26 (0.38), residues: 217 sheet: -1.27 (0.47), residues: 136 loop : -2.15 (0.27), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 213 HIS 0.002 0.000 HIS A 837 PHE 0.009 0.001 PHE A 148 TYR 0.012 0.001 TYR A 204 ARG 0.004 0.000 ARG A 599 *********************** 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 108 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 81 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 TYR cc_start: 0.8025 (t80) cc_final: 0.7788 (t80) REVERT: A 208 GLU cc_start: 0.8363 (tm-30) cc_final: 0.7965 (tm-30) REVERT: A 345 GLN cc_start: 0.9548 (pt0) cc_final: 0.9119 (pp30) REVERT: A 444 MET cc_start: 0.6311 (mmp) cc_final: 0.5817 (mmp) REVERT: A 506 GLU cc_start: 0.8742 (tp30) cc_final: 0.8533 (tp30) REVERT: A 550 MET cc_start: 0.8032 (mmm) cc_final: 0.7671 (mmm) REVERT: A 575 GLU cc_start: 0.8543 (tp30) cc_final: 0.8323 (tp30) REVERT: A 599 ARG cc_start: 0.8564 (mtp85) cc_final: 0.8090 (mtp85) REVERT: A 793 TYR cc_start: 0.8628 (OUTLIER) cc_final: 0.7936 (t80) REVERT: A 896 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8705 (mm) REVERT: A 932 TYR cc_start: 0.8432 (OUTLIER) cc_final: 0.7870 (t80) outliers start: 27 outliers final: 16 residues processed: 103 average time/residue: 0.1903 time to fit residues: 26.7441 Evaluate side-chains 95 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 932 TYR 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: 0.2980 chunk 39 optimal weight: 0.7980 chunk 8 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- 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** A 900 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.119368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.087432 restraints weight = 16443.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.090066 restraints weight = 8461.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.091731 restraints weight = 5665.928| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7212 Z= 0.264 Angle : 0.634 7.962 9917 Z= 0.329 Chirality : 0.043 0.184 1139 Planarity : 0.004 0.038 1150 Dihedral : 17.715 178.728 1382 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 4.06 % Allowed : 18.84 % Favored : 77.10 % 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: -2.02 (0.29), residues: 779 helix: 0.19 (0.38), residues: 216 sheet: -1.30 (0.48), residues: 133 loop : -2.24 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 213 HIS 0.002 0.001 HIS A 894 PHE 0.013 0.002 PHE A 874 TYR 0.010 0.002 TYR A 738 ARG 0.005 0.000 ARG A 599 *********************** 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 100 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 72 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 TYR cc_start: 0.8091 (t80) cc_final: 0.7846 (t80) REVERT: A 208 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8149 (tm-30) REVERT: A 337 LEU cc_start: 0.7668 (tp) cc_final: 0.7165 (tp) REVERT: A 341 GLU cc_start: 0.8359 (pm20) cc_final: 0.7991 (pm20) REVERT: A 432 GLN cc_start: 0.6936 (OUTLIER) cc_final: 0.6389 (mp10) REVERT: A 444 MET cc_start: 0.6474 (mmp) cc_final: 0.6208 (mmp) REVERT: A 506 GLU cc_start: 0.8764 (tp30) cc_final: 0.8523 (tp30) REVERT: A 550 MET cc_start: 0.8150 (mmm) cc_final: 0.7594 (mmm) REVERT: A 575 GLU cc_start: 0.8662 (tp30) cc_final: 0.8425 (tp30) REVERT: A 623 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8517 (mm) REVERT: A 793 TYR cc_start: 0.8665 (OUTLIER) cc_final: 0.7887 (t80) REVERT: A 896 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8721 (mm) REVERT: A 932 TYR cc_start: 0.8615 (OUTLIER) cc_final: 0.8001 (t80) outliers start: 28 outliers final: 19 residues processed: 96 average time/residue: 0.2019 time to fit residues: 26.4441 Evaluate side-chains 89 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 0.780 ------------------------------------------------------------------------------- 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 432 GLN Chi-restraints excluded: chain A residue 479 GLU 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 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 858 ILE 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: 5.9990 chunk 56 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 74 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 63 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3931 r_free = 0.3931 target = 0.122490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.090794 restraints weight = 16423.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.093597 restraints weight = 8320.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.095374 restraints weight = 5469.990| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7212 Z= 0.156 Angle : 0.592 7.867 9917 Z= 0.303 Chirality : 0.042 0.186 1139 Planarity : 0.004 0.038 1150 Dihedral : 17.647 179.686 1382 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 3.62 % Allowed : 20.72 % Favored : 75.65 % 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: -1.91 (0.30), residues: 779 helix: 0.27 (0.38), residues: 217 sheet: -1.42 (0.46), residues: 140 loop : -2.10 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 213 HIS 0.002 0.000 HIS A 892 PHE 0.009 0.001 PHE A 148 TYR 0.011 0.001 TYR A 893 ARG 0.002 0.000 ARG A 361 *********************** 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 106 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 81 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.8485 (tm-30) cc_final: 0.8059 (tm-30) REVERT: A 345 GLN cc_start: 0.9540 (pt0) cc_final: 0.9155 (pp30) REVERT: A 432 GLN cc_start: 0.6596 (OUTLIER) cc_final: 0.6091 (mp10) REVERT: A 444 MET cc_start: 0.6442 (mmp) cc_final: 0.6172 (mmt) REVERT: A 506 GLU cc_start: 0.8768 (tp30) cc_final: 0.8550 (tp30) REVERT: A 550 MET cc_start: 0.7961 (mmm) cc_final: 0.7685 (mmm) REVERT: A 579 MET cc_start: 0.8035 (tpp) cc_final: 0.7599 (tpp) REVERT: A 732 TRP cc_start: 0.6698 (t-100) cc_final: 0.6259 (t-100) REVERT: A 932 TYR cc_start: 0.8459 (OUTLIER) cc_final: 0.7769 (t80) outliers start: 25 outliers final: 17 residues processed: 99 average time/residue: 0.1837 time to fit residues: 25.1250 Evaluate side-chains 90 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 375 VAL Chi-restraints excluded: chain A residue 432 GLN 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 671 ASN Chi-restraints excluded: chain A residue 687 LEU 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 838 HIS Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 869 CYS 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: 4.9990 chunk 65 optimal weight: 0.6980 chunk 10 optimal weight: 20.0000 chunk 62 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 80 optimal weight: 30.0000 chunk 14 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 overall best weight: 3.0786 ------------------------------------------------------------------------------- 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 = 0.3865 r_free = 0.3865 target = 0.118455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.085806 restraints weight = 16266.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.088459 restraints weight = 8342.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.090148 restraints weight = 5551.247| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7212 Z= 0.295 Angle : 0.675 9.488 9917 Z= 0.347 Chirality : 0.044 0.185 1139 Planarity : 0.004 0.039 1150 Dihedral : 17.716 178.813 1382 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 4.20 % Allowed : 20.87 % 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: -2.11 (0.29), residues: 779 helix: 0.15 (0.37), residues: 217 sheet: -1.50 (0.44), residues: 146 loop : -2.27 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 213 HIS 0.002 0.001 HIS A 837 PHE 0.014 0.002 PHE A 874 TYR 0.046 0.002 TYR A 197 ARG 0.004 0.000 ARG A 175 *********************** 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 94 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 65 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 TRP cc_start: 0.8296 (t60) cc_final: 0.7923 (t60) REVERT: A 432 GLN cc_start: 0.7002 (OUTLIER) cc_final: 0.6439 (mp10) REVERT: A 550 MET cc_start: 0.8195 (mmm) cc_final: 0.7804 (mmm) REVERT: A 552 VAL cc_start: 0.8702 (OUTLIER) cc_final: 0.8318 (p) REVERT: A 932 TYR cc_start: 0.8617 (OUTLIER) cc_final: 0.8006 (t80) outliers start: 29 outliers final: 20 residues processed: 89 average time/residue: 0.1770 time to fit residues: 22.1446 Evaluate side-chains 88 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LEU 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 552 VAL 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 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 858 ILE Chi-restraints excluded: chain A residue 869 CYS 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: 4.9990 chunk 66 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.3889 r_free = 0.3889 target = 0.119990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.087459 restraints weight = 16335.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.090166 restraints weight = 8319.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.091879 restraints weight = 5485.425| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3489 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= 0.221 Angle : 0.647 8.644 9917 Z= 0.330 Chirality : 0.043 0.185 1139 Planarity : 0.004 0.039 1150 Dihedral : 17.702 179.959 1382 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 3.91 % Allowed : 21.59 % 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: -2.05 (0.29), residues: 779 helix: 0.20 (0.37), residues: 217 sheet: -1.47 (0.44), residues: 148 loop : -2.24 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 213 HIS 0.002 0.001 HIS A 892 PHE 0.015 0.001 PHE A 902 TYR 0.038 0.002 TYR A 197 ARG 0.002 0.000 ARG A 942 *********************** 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: 27 poor density : 75 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8078 (tm-30) REVERT: A 432 GLN cc_start: 0.6917 (OUTLIER) cc_final: 0.6378 (mp10) REVERT: A 550 MET cc_start: 0.8130 (mmm) cc_final: 0.7762 (mmm) REVERT: A 552 VAL cc_start: 0.8484 (OUTLIER) cc_final: 0.7984 (p) REVERT: A 932 TYR cc_start: 0.8531 (OUTLIER) cc_final: 0.7852 (t80) outliers start: 27 outliers final: 19 residues processed: 96 average time/residue: 0.1745 time to fit residues: 23.5972 Evaluate side-chains 91 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 1.364 ------------------------------------------------------------------------------- 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 552 VAL 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 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 858 ILE Chi-restraints excluded: chain A residue 869 CYS 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: 5.9990 chunk 69 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3948 r_free = 0.3948 target = 0.125426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.090545 restraints weight = 16384.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.093475 restraints weight = 8217.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.095330 restraints weight = 5410.253| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7212 Z= 0.163 Angle : 0.625 9.224 9917 Z= 0.315 Chirality : 0.042 0.186 1139 Planarity : 0.004 0.038 1150 Dihedral : 17.616 178.746 1382 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 2.90 % Allowed : 23.19 % Favored : 73.91 % 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: -1.86 (0.30), residues: 779 helix: 0.30 (0.37), residues: 218 sheet: -1.31 (0.45), residues: 148 loop : -2.11 (0.28), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 213 HIS 0.002 0.000 HIS A 892 PHE 0.010 0.001 PHE A 148 TYR 0.033 0.001 TYR A 197 ARG 0.003 0.000 ARG A 942 ********************** 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 106 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8128 (tm-30) REVERT: A 432 GLN cc_start: 0.6912 (OUTLIER) cc_final: 0.6369 (mp10) REVERT: A 506 GLU cc_start: 0.8948 (tp30) cc_final: 0.8735 (tp30) REVERT: A 550 MET cc_start: 0.8151 (mmm) cc_final: 0.7740 (mmm) REVERT: A 579 MET cc_start: 0.8126 (tpp) cc_final: 0.7730 (tpp) REVERT: A 732 TRP cc_start: 0.6817 (t-100) cc_final: 0.6044 (t-100) REVERT: A 932 TYR cc_start: 0.8391 (OUTLIER) cc_final: 0.7635 (t80) outliers start: 20 outliers final: 14 residues processed: 98 average time/residue: 0.1747 time to fit residues: 23.8694 Evaluate side-chains 93 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.769 ------------------------------------------------------------------------------- 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 432 GLN 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 701 ILE Chi-restraints excluded: chain A residue 793 TYR Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 869 CYS 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: 6.9990 chunk 66 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3875 r_free = 0.3875 target = 0.118736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.085669 restraints weight = 16364.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.088399 restraints weight = 8159.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.090196 restraints weight = 5356.282| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7212 Z= 0.312 Angle : 0.686 9.498 9917 Z= 0.353 Chirality : 0.045 0.185 1139 Planarity : 0.004 0.038 1150 Dihedral : 17.697 179.518 1382 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 3.33 % Allowed : 22.75 % Favored : 73.91 % 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: -2.02 (0.29), residues: 779 helix: 0.21 (0.37), residues: 216 sheet: -1.39 (0.45), residues: 148 loop : -2.24 (0.27), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 213 HIS 0.003 0.001 HIS A 251 PHE 0.018 0.002 PHE A 333 TYR 0.033 0.002 TYR A 197 ARG 0.003 0.000 ARG A 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2174.46 seconds wall clock time: 40 minutes 0.66 seconds (2400.66 seconds total)