Starting phenix.real_space_refine on Tue Feb 13 16:54:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swq_25482/02_2024/7swq_25482.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swq_25482/02_2024/7swq_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swq_25482/02_2024/7swq_25482.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swq_25482/02_2024/7swq_25482.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swq_25482/02_2024/7swq_25482.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swq_25482/02_2024/7swq_25482.pdb" } 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 Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 590": "OE1" <-> "OE2" Residue "A ASP 601": "OD1" <-> "OD2" Residue "A GLU 604": "OE1" <-> "OE2" Residue "A TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 734": "OE1" <-> "OE2" Residue "A TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 750": "OE1" <-> "OE2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 893": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 939": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 4.50, per 1000 atoms: 0.64 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 - 3.50 Amino acid : False - 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: 3.13 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: 2.54 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: 2.76 Time building geometry restraints manager: 3.30 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: 98.98 - 105.98: 346 105.98 - 112.98: 3938 112.98 - 119.98: 2441 119.98 - 126.98: 3045 126.98 - 133.98: 147 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 2.440 nonbonded pdb=" NH2 ARG A 940 " pdb=" OH TYR A 944 " model vdw 2.200 2.520 nonbonded pdb=" NH2 ARG A 920 " pdb=" OP1 G B 3 " model vdw 2.202 2.520 ... (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 ========== 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.050 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 25.280 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.940 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.786 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: 0.2140 time to fit residues: 36.1015 Evaluate side-chains 82 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.703 ------------------------------------------------------------------------------- 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: 0.7980 chunk 21 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 64 optimal weight: 0.1980 chunk 24 optimal weight: 0.0570 chunk 39 optimal weight: 0.9980 chunk 47 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 GLN A 609 HIS A 823 ASN A 846 HIS A 900 ASN ** A 901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7212 Z= 0.160 Angle : 0.601 7.835 9917 Z= 0.306 Chirality : 0.041 0.189 1139 Planarity : 0.004 0.037 1150 Dihedral : 17.864 179.552 1382 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 1.59 % Allowed : 10.72 % Favored : 87.68 % 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: -1.98 (0.30), residues: 779 helix: 0.11 (0.38), residues: 214 sheet: -1.31 (0.48), residues: 130 loop : -2.12 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 759 HIS 0.007 0.001 HIS A 609 PHE 0.011 0.001 PHE A 311 TYR 0.013 0.001 TYR A 932 ARG 0.007 0.000 ARG A 300 *********************** 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 105 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 277 GLU cc_start: 0.7465 (tt0) cc_final: 0.7243 (tt0) REVERT: A 444 MET cc_start: 0.4194 (mmp) cc_final: 0.3839 (mmp) REVERT: A 506 GLU cc_start: 0.7225 (pm20) cc_final: 0.6996 (pm20) REVERT: A 567 ASN cc_start: 0.7074 (t0) cc_final: 0.6849 (t0) outliers start: 11 outliers final: 9 residues processed: 101 average time/residue: 0.2012 time to fit residues: 27.5708 Evaluate side-chains 89 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 0.705 ------------------------------------------------------------------------------- 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 358 ASP Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 655 CYS Chi-restraints excluded: chain A residue 684 ASN Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 819 SER 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 41 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 74 optimal weight: 0.8980 chunk 80 optimal weight: 30.0000 chunk 66 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 chunk 25 optimal weight: 0.0370 chunk 59 optimal weight: 10.0000 overall best weight: 1.7662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 870 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7212 Z= 0.201 Angle : 0.589 7.107 9917 Z= 0.304 Chirality : 0.042 0.189 1139 Planarity : 0.004 0.037 1150 Dihedral : 17.777 178.430 1382 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 2.61 % Allowed : 14.06 % Favored : 83.33 % 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: -1.94 (0.29), residues: 779 helix: 0.13 (0.37), residues: 217 sheet: -1.21 (0.49), residues: 128 loop : -2.13 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 213 HIS 0.002 0.001 HIS A 870 PHE 0.013 0.001 PHE A 874 TYR 0.025 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 106 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 88 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7272 (pp) REVERT: A 444 MET cc_start: 0.4372 (mmp) cc_final: 0.4137 (mmp) REVERT: A 550 MET cc_start: 0.6983 (mmm) cc_final: 0.6737 (mmm) REVERT: A 567 ASN cc_start: 0.7193 (t0) cc_final: 0.6980 (t0) REVERT: A 616 ASN cc_start: 0.7804 (m-40) cc_final: 0.7563 (m-40) REVERT: A 793 TYR cc_start: 0.8032 (OUTLIER) cc_final: 0.7777 (t80) outliers start: 18 outliers final: 12 residues processed: 98 average time/residue: 0.1936 time to fit residues: 25.8888 Evaluate side-chains 89 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 75 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 358 ASP Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 655 CYS Chi-restraints excluded: chain A residue 684 ASN 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 819 SER 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 73 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 21 optimal weight: 20.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 870 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7212 Z= 0.274 Angle : 0.626 7.414 9917 Z= 0.326 Chirality : 0.043 0.190 1139 Planarity : 0.004 0.037 1150 Dihedral : 17.844 177.732 1382 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 3.48 % Allowed : 15.94 % Favored : 80.58 % 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: 0.15 (0.37), residues: 219 sheet: -1.23 (0.50), residues: 128 loop : -2.13 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 213 HIS 0.002 0.001 HIS A 488 PHE 0.016 0.002 PHE A 874 TYR 0.018 0.002 TYR A 204 ARG 0.003 0.000 ARG A 276 *********************** 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 100 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 76 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ILE cc_start: 0.6245 (OUTLIER) cc_final: 0.5931 (mm) REVERT: A 442 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7455 (pp) REVERT: A 444 MET cc_start: 0.4393 (mmp) cc_final: 0.3594 (mmp) REVERT: A 616 ASN cc_start: 0.7889 (m-40) cc_final: 0.7571 (m-40) REVERT: A 793 TYR cc_start: 0.8075 (OUTLIER) cc_final: 0.7711 (t80) outliers start: 24 outliers final: 16 residues processed: 93 average time/residue: 0.1947 time to fit residues: 24.7750 Evaluate side-chains 89 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 70 time to evaluate : 0.788 ------------------------------------------------------------------------------- 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 358 ASP Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 655 CYS Chi-restraints excluded: chain A residue 684 ASN 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 731 ASP Chi-restraints excluded: chain A residue 793 TYR Chi-restraints excluded: chain A residue 819 SER 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 974 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 823 ASN ** A 870 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2942 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= 0.267 Angle : 0.617 7.883 9917 Z= 0.320 Chirality : 0.043 0.191 1139 Planarity : 0.004 0.038 1150 Dihedral : 17.874 178.288 1382 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 4.35 % Allowed : 16.96 % Favored : 78.70 % 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: 221 sheet: -1.27 (0.49), residues: 128 loop : -2.18 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 213 HIS 0.002 0.001 HIS A 837 PHE 0.014 0.002 PHE A 874 TYR 0.013 0.002 TYR A 932 ARG 0.002 0.000 ARG A 361 *********************** 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 102 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 72 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ILE cc_start: 0.6127 (OUTLIER) cc_final: 0.5825 (mm) REVERT: A 442 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7498 (pp) REVERT: A 444 MET cc_start: 0.4430 (mmp) cc_final: 0.3737 (mmp) REVERT: A 616 ASN cc_start: 0.7925 (m-40) cc_final: 0.7613 (m-40) REVERT: A 732 TRP cc_start: 0.5835 (t-100) cc_final: 0.5373 (t-100) REVERT: A 793 TYR cc_start: 0.7989 (OUTLIER) cc_final: 0.7565 (t80) REVERT: A 830 PHE cc_start: 0.7934 (OUTLIER) cc_final: 0.7490 (t80) REVERT: A 932 TYR cc_start: 0.8216 (OUTLIER) cc_final: 0.7980 (t80) outliers start: 30 outliers final: 16 residues processed: 95 average time/residue: 0.1642 time to fit residues: 22.4064 Evaluate side-chains 89 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 68 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 358 ASP Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 655 CYS Chi-restraints excluded: chain A residue 684 ASN 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 731 ASP Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 793 TYR Chi-restraints excluded: chain A residue 819 SER 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 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 26 optimal weight: 20.0000 chunk 71 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 0.0980 chunk 19 optimal weight: 7.9990 chunk 79 optimal weight: 8.9990 chunk 65 optimal weight: 0.8980 chunk 36 optimal weight: 0.4980 chunk 6 optimal weight: 6.9990 chunk 41 optimal weight: 0.0980 chunk 76 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 870 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3121 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= 0.147 Angle : 0.579 8.597 9917 Z= 0.297 Chirality : 0.041 0.189 1139 Planarity : 0.004 0.038 1150 Dihedral : 17.740 179.928 1382 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 3.33 % Allowed : 19.13 % Favored : 77.54 % 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: -1.77 (0.30), residues: 779 helix: 0.39 (0.38), residues: 222 sheet: -1.29 (0.47), residues: 133 loop : -2.06 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 213 HIS 0.002 0.000 HIS A 870 PHE 0.008 0.001 PHE A 572 TYR 0.011 0.001 TYR A 204 ARG 0.002 0.000 ARG A 361 *********************** 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 102 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 79 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ILE cc_start: 0.6124 (OUTLIER) cc_final: 0.5839 (mm) REVERT: A 442 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7439 (pp) REVERT: A 444 MET cc_start: 0.4310 (mmp) cc_final: 0.3709 (mmp) REVERT: A 616 ASN cc_start: 0.7933 (m-40) cc_final: 0.7647 (m-40) REVERT: A 732 TRP cc_start: 0.5586 (t-100) cc_final: 0.5174 (t-100) REVERT: A 830 PHE cc_start: 0.7838 (OUTLIER) cc_final: 0.7431 (t80) outliers start: 23 outliers final: 17 residues processed: 96 average time/residue: 0.1643 time to fit residues: 22.8180 Evaluate side-chains 89 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 69 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 358 ASP Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 655 CYS Chi-restraints excluded: chain A residue 684 ASN Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 731 ASP Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 793 TYR Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 869 CYS 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 8 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 49 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 870 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7212 Z= 0.284 Angle : 0.635 7.908 9917 Z= 0.330 Chirality : 0.043 0.192 1139 Planarity : 0.004 0.038 1150 Dihedral : 17.827 178.508 1382 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer: Outliers : 4.64 % Allowed : 18.84 % Favored : 76.52 % 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 (0.29), residues: 779 helix: 0.30 (0.37), residues: 220 sheet: -1.25 (0.48), residues: 128 loop : -2.20 (0.27), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 213 HIS 0.003 0.001 HIS A 837 PHE 0.014 0.002 PHE A 874 TYR 0.017 0.002 TYR A 932 ARG 0.003 0.000 ARG A 276 *********************** 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 109 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 77 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ILE cc_start: 0.6172 (OUTLIER) cc_final: 0.5945 (mm) REVERT: A 442 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7543 (pp) REVERT: A 444 MET cc_start: 0.4415 (mmp) cc_final: 0.3828 (mmp) REVERT: A 616 ASN cc_start: 0.7876 (m-40) cc_final: 0.7623 (m-40) REVERT: A 732 TRP cc_start: 0.5973 (t-100) cc_final: 0.5714 (t-100) outliers start: 32 outliers final: 22 residues processed: 102 average time/residue: 0.1619 time to fit residues: 23.5603 Evaluate side-chains 92 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 68 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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 186 LYS 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 358 ASP Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 655 CYS Chi-restraints excluded: chain A residue 684 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 731 ASP Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 793 TYR Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 869 CYS 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 23 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 870 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7212 Z= 0.228 Angle : 0.603 8.198 9917 Z= 0.313 Chirality : 0.042 0.191 1139 Planarity : 0.004 0.038 1150 Dihedral : 17.818 179.589 1382 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 4.64 % Allowed : 19.42 % Favored : 75.94 % 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: -1.79 (0.29), residues: 779 helix: 0.51 (0.38), residues: 214 sheet: -1.10 (0.49), residues: 124 loop : -2.18 (0.26), residues: 441 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 148 TYR 0.014 0.001 TYR A 932 ARG 0.002 0.000 ARG A 276 *********************** 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 106 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 74 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 ILE cc_start: 0.6169 (OUTLIER) cc_final: 0.5946 (mm) REVERT: A 442 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7537 (pp) REVERT: A 444 MET cc_start: 0.4502 (mmp) cc_final: 0.4054 (mmp) REVERT: A 616 ASN cc_start: 0.7863 (m-40) cc_final: 0.7642 (m-40) REVERT: A 732 TRP cc_start: 0.5866 (t-100) cc_final: 0.5635 (t-100) outliers start: 32 outliers final: 21 residues processed: 99 average time/residue: 0.1662 time to fit residues: 23.5412 Evaluate side-chains 96 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 73 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 358 ASP Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 655 CYS Chi-restraints excluded: chain A residue 684 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 731 ASP Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 793 TYR Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 869 CYS 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 75 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 57 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 47 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 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 GLN ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 870 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7212 Z= 0.230 Angle : 0.630 9.746 9917 Z= 0.322 Chirality : 0.043 0.191 1139 Planarity : 0.004 0.044 1150 Dihedral : 17.847 179.872 1382 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer: Outliers : 3.62 % Allowed : 21.74 % Favored : 74.64 % 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: -1.78 (0.29), residues: 779 helix: 0.57 (0.38), residues: 214 sheet: -1.23 (0.48), residues: 129 loop : -2.16 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 213 HIS 0.002 0.001 HIS A 488 PHE 0.015 0.001 PHE A 148 TYR 0.019 0.002 TYR A 185 ARG 0.005 0.000 ARG A 183 *********************** 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 99 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 74 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 ILE cc_start: 0.6084 (OUTLIER) cc_final: 0.5856 (mm) REVERT: A 442 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7544 (pp) REVERT: A 444 MET cc_start: 0.4486 (mmp) cc_final: 0.4049 (mmp) REVERT: A 487 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7702 (mm-40) REVERT: A 732 TRP cc_start: 0.5853 (t-100) cc_final: 0.5649 (t-100) outliers start: 25 outliers final: 21 residues processed: 93 average time/residue: 0.1512 time to fit residues: 20.6735 Evaluate side-chains 96 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 72 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 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 358 ASP Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 655 CYS Chi-restraints excluded: chain A residue 684 ASN Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 731 ASP Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 793 TYR Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 869 CYS 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 36 optimal weight: 7.9990 chunk 54 optimal weight: 0.6980 chunk 81 optimal weight: 10.0000 chunk 75 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 GLN ** A 870 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3576 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= 0.176 Angle : 0.609 9.589 9917 Z= 0.309 Chirality : 0.041 0.190 1139 Planarity : 0.004 0.043 1150 Dihedral : 17.789 179.484 1382 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 3.62 % Allowed : 22.03 % Favored : 74.35 % 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: -1.64 (0.30), residues: 779 helix: 0.78 (0.38), residues: 215 sheet: -1.23 (0.45), residues: 142 loop : -2.12 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 213 HIS 0.002 0.001 HIS A 488 PHE 0.018 0.001 PHE A 148 TYR 0.021 0.001 TYR A 185 ARG 0.006 0.000 ARG A 183 ********************** 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 fitting. rotamer outliers: 25 poor density : 78 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 ILE cc_start: 0.6069 (OUTLIER) cc_final: 0.5836 (mm) REVERT: A 442 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7502 (pp) REVERT: A 444 MET cc_start: 0.4408 (mmp) cc_final: 0.4065 (mmp) outliers start: 25 outliers final: 21 residues processed: 97 average time/residue: 0.1598 time to fit residues: 22.2764 Evaluate side-chains 96 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 73 time to evaluate : 0.785 ------------------------------------------------------------------------------- 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 358 ASP Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 655 CYS Chi-restraints excluded: chain A residue 684 ASN Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 731 ASP Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 793 TYR Chi-restraints excluded: chain A residue 819 SER Chi-restraints excluded: chain A residue 869 CYS 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 59 optimal weight: 9.9990 chunk 9 optimal weight: 20.0000 chunk 18 optimal weight: 4.9990 chunk 65 optimal weight: 0.1980 chunk 27 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 3 optimal weight: 20.0000 chunk 47 optimal weight: 8.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 GLN ** 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 = 0.119644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.087138 restraints weight = 16072.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.089834 restraints weight = 8222.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.091486 restraints weight = 5423.320| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 7212 Z= 0.312 Angle : 0.670 9.354 9917 Z= 0.343 Chirality : 0.044 0.193 1139 Planarity : 0.005 0.042 1150 Dihedral : 17.875 179.423 1382 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 4.06 % Allowed : 22.03 % 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: -1.76 (0.29), residues: 779 helix: 0.65 (0.37), residues: 214 sheet: -1.23 (0.47), residues: 129 loop : -2.18 (0.26), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP A 732 HIS 0.008 0.001 HIS A 488 PHE 0.015 0.002 PHE A 874 TYR 0.021 0.002 TYR A 185 ARG 0.007 0.000 ARG A 183 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1431.88 seconds wall clock time: 26 minutes 54.38 seconds (1614.38 seconds total)