Starting phenix.real_space_refine on Sat Nov 16 12:54:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fy9_29561/11_2024/8fy9_29561.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fy9_29561/11_2024/8fy9_29561.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fy9_29561/11_2024/8fy9_29561.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fy9_29561/11_2024/8fy9_29561.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fy9_29561/11_2024/8fy9_29561.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fy9_29561/11_2024/8fy9_29561.cif" } resolution = 3.1 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= -0.001 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 611 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 54 5.49 5 S 30 5.16 5 C 6628 2.51 5 N 1942 2.21 5 O 2088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 10742 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 746 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain: "B" Number of atoms: 1865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1865 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 8, 'TRANS': 232} Chain breaks: 1 Chain: "C" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2186 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain: "D" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 746 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain: "E" Number of atoms: 1865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1865 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 8, 'TRANS': 232} Chain breaks: 1 Chain: "F" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2186 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain: "G" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 573 Classifications: {'DNA': 28} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 27} Chain: "H" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 575 Classifications: {'DNA': 28} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 27} Time building chain proxies: 7.51, per 1000 atoms: 0.70 Number of scatterers: 10742 At special positions: 0 Unit cell: (94.775, 90.315, 142.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 54 15.00 O 2088 8.00 N 1942 7.00 C 6628 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.76 Conformation dependent library (CDL) restraints added in 1.3 seconds 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2268 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 9 sheets defined 51.1% alpha, 14.8% beta 11 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 3.82 Creating SS restraints... Processing helix chain 'A' and resid 12 through 19 Processing helix chain 'A' and resid 36 through 51 Processing helix chain 'B' and resid 68 through 77 Processing helix chain 'B' and resid 86 through 89 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 102 through 114 removed outlier: 4.070A pdb=" N ASN B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 129 Processing helix chain 'B' and resid 182 through 205 Processing helix chain 'B' and resid 219 through 230 removed outlier: 3.616A pdb=" N TYR B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 244 Processing helix chain 'B' and resid 250 through 264 Processing helix chain 'B' and resid 266 through 280 Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'C' and resid 17 through 21 removed outlier: 3.729A pdb=" N ARG C 21 " --> pdb=" O VAL C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 53 No H-bonds generated for 'chain 'C' and resid 51 through 53' Processing helix chain 'C' and resid 68 through 78 Processing helix chain 'C' and resid 102 through 114 removed outlier: 3.641A pdb=" N ASN C 114 " --> pdb=" O GLU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 130 Processing helix chain 'C' and resid 139 through 163 Processing helix chain 'C' and resid 180 through 205 Processing helix chain 'C' and resid 219 through 231 removed outlier: 3.954A pdb=" N LEU C 228 " --> pdb=" O ASP C 224 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N TYR C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ALA C 231 " --> pdb=" O ASP C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 245 Processing helix chain 'C' and resid 250 through 267 Processing helix chain 'C' and resid 267 through 280 Processing helix chain 'D' and resid 12 through 19 Processing helix chain 'D' and resid 20 through 22 No H-bonds generated for 'chain 'D' and resid 20 through 22' Processing helix chain 'D' and resid 36 through 51 Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'E' and resid 67 through 77 Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 102 through 114 removed outlier: 3.922A pdb=" N ASN E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 129 Processing helix chain 'E' and resid 182 through 205 Processing helix chain 'E' and resid 219 through 227 Processing helix chain 'E' and resid 233 through 245 Processing helix chain 'E' and resid 250 through 264 removed outlier: 3.945A pdb=" N LEU E 254 " --> pdb=" O ASP E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 280 removed outlier: 3.748A pdb=" N LEU E 280 " --> pdb=" O LEU E 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 21 removed outlier: 3.724A pdb=" N ARG F 21 " --> pdb=" O VAL F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 53 No H-bonds generated for 'chain 'F' and resid 51 through 53' Processing helix chain 'F' and resid 67 through 78 removed outlier: 3.868A pdb=" N VAL F 71 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 114 removed outlier: 3.760A pdb=" N ASN F 114 " --> pdb=" O GLU F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 130 Processing helix chain 'F' and resid 139 through 163 Processing helix chain 'F' and resid 180 through 205 Processing helix chain 'F' and resid 219 through 231 removed outlier: 4.476A pdb=" N LEU F 228 " --> pdb=" O ASP F 224 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TYR F 229 " --> pdb=" O VAL F 225 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA F 231 " --> pdb=" O ASP F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 245 Processing helix chain 'F' and resid 250 through 267 Processing helix chain 'F' and resid 267 through 280 removed outlier: 3.745A pdb=" N LEU F 280 " --> pdb=" O LEU F 276 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27 removed outlier: 5.291A pdb=" N GLU A 25 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL A 32 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA A 27 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N MET A 3 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA A 61 " --> pdb=" O MET A 3 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 81 removed outlier: 5.277A pdb=" N ILE A 88 " --> pdb=" O ARG F 49 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ARG F 49 " --> pdb=" O ILE A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 289 through 291 removed outlier: 8.053A pdb=" N VAL B 57 " --> pdb=" O ARG B 21 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR B 23 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N LEU B 59 " --> pdb=" O THR B 23 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE B 25 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU B 58 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL B 84 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU B 60 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TRP C 83 " --> pdb=" O ARG C 90 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N TYR C 92 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU C 81 " --> pdb=" O TYR C 92 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR C 23 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LEU C 59 " --> pdb=" O THR C 23 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE C 25 " --> pdb=" O LEU C 59 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 39 through 41 removed outlier: 7.627A pdb=" N ALA B 30 " --> pdb=" O ASP B 65 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N SER B 67 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ILE B 32 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ARG C 34 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS C 31 " --> pdb=" O ALA C 42 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG C 49 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ILE D 88 " --> pdb=" O ARG C 49 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 49 removed outlier: 3.939A pdb=" N ASN B 308 " --> pdb=" O ARG B 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 24 through 27 removed outlier: 5.588A pdb=" N GLU D 25 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL D 32 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA D 27 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N MET D 3 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA D 61 " --> pdb=" O MET D 3 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 91 through 94 removed outlier: 6.563A pdb=" N TRP E 83 " --> pdb=" O TYR E 92 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N SER E 94 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU E 81 " --> pdb=" O SER E 94 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU E 58 " --> pdb=" O VAL E 82 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL E 84 " --> pdb=" O LEU E 58 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU E 60 " --> pdb=" O VAL E 84 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N VAL E 57 " --> pdb=" O ARG E 21 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N THR E 23 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N LEU E 59 " --> pdb=" O THR E 23 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE E 25 " --> pdb=" O LEU E 59 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 32 through 35 Processing sheet with id=AA9, first strand: chain 'F' and resid 22 through 27 removed outlier: 6.349A pdb=" N THR F 23 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N LEU F 59 " --> pdb=" O THR F 23 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ILE F 25 " --> pdb=" O LEU F 59 " (cutoff:3.500A) 525 hydrogen bonds defined for protein. 1512 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 3.68 Time building geometry restraints manager: 3.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3117 1.34 - 1.45: 1970 1.45 - 1.57: 5799 1.57 - 1.69: 108 1.69 - 1.81: 58 Bond restraints: 11052 Sorted by residual: bond pdb=" C3' DC G 8 " pdb=" O3' DC G 8 " ideal model delta sigma weight residual 1.422 1.463 -0.041 3.00e-02 1.11e+03 1.83e+00 bond pdb=" C4' DG H 24 " pdb=" O4' DG H 24 " ideal model delta sigma weight residual 1.450 1.432 0.018 2.00e-02 2.50e+03 7.88e-01 bond pdb=" O4' DT H 3 " pdb=" C1' DT H 3 " ideal model delta sigma weight residual 1.414 1.396 0.018 2.00e-02 2.50e+03 7.79e-01 bond pdb=" C4' DG G 24 " pdb=" O4' DG G 24 " ideal model delta sigma weight residual 1.450 1.433 0.017 2.00e-02 2.50e+03 7.62e-01 bond pdb=" C4' DC H 2 " pdb=" O4' DC H 2 " ideal model delta sigma weight residual 1.450 1.433 0.017 2.00e-02 2.50e+03 7.47e-01 ... (remaining 11047 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 15004 1.98 - 3.96: 168 3.96 - 5.94: 18 5.94 - 7.92: 4 7.92 - 9.90: 2 Bond angle restraints: 15196 Sorted by residual: angle pdb=" CB ARG F 150 " pdb=" CG ARG F 150 " pdb=" CD ARG F 150 " ideal model delta sigma weight residual 111.30 121.20 -9.90 2.30e+00 1.89e-01 1.85e+01 angle pdb=" N GLU C 147 " pdb=" CA GLU C 147 " pdb=" CB GLU C 147 " ideal model delta sigma weight residual 110.12 115.11 -4.99 1.47e+00 4.63e-01 1.15e+01 angle pdb=" CA GLU C 147 " pdb=" CB GLU C 147 " pdb=" CG GLU C 147 " ideal model delta sigma weight residual 114.10 119.17 -5.07 2.00e+00 2.50e-01 6.44e+00 angle pdb=" C GLU C 232 " pdb=" N ILE C 233 " pdb=" CA ILE C 233 " ideal model delta sigma weight residual 123.16 120.59 2.57 1.06e+00 8.90e-01 5.86e+00 angle pdb=" CA GLN F 87 " pdb=" CB GLN F 87 " pdb=" CG GLN F 87 " ideal model delta sigma weight residual 114.10 118.84 -4.74 2.00e+00 2.50e-01 5.61e+00 ... (remaining 15191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.42: 6184 34.42 - 68.83: 314 68.83 - 103.25: 9 103.25 - 137.66: 0 137.66 - 172.08: 1 Dihedral angle restraints: 6508 sinusoidal: 2974 harmonic: 3534 Sorted by residual: dihedral pdb=" CA ARG E 34 " pdb=" C ARG E 34 " pdb=" N VAL E 35 " pdb=" CA VAL E 35 " ideal model delta harmonic sigma weight residual 180.00 156.58 23.42 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" C4' DC G 8 " pdb=" C3' DC G 8 " pdb=" O3' DC G 8 " pdb=" P DT G 9 " ideal model delta sinusoidal sigma weight residual 220.00 47.92 172.08 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA ASP D 81 " pdb=" CB ASP D 81 " pdb=" CG ASP D 81 " pdb=" OD1 ASP D 81 " ideal model delta sinusoidal sigma weight residual -30.00 -89.67 59.67 1 2.00e+01 2.50e-03 1.19e+01 ... (remaining 6505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1428 0.050 - 0.100: 245 0.100 - 0.150: 51 0.150 - 0.199: 1 0.199 - 0.249: 1 Chirality restraints: 1726 Sorted by residual: chirality pdb=" CA ARG F 150 " pdb=" N ARG F 150 " pdb=" C ARG F 150 " pdb=" CB ARG F 150 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CB VAL C 191 " pdb=" CA VAL C 191 " pdb=" CG1 VAL C 191 " pdb=" CG2 VAL C 191 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.19 2.00e-01 2.50e+01 9.43e-01 chirality pdb=" CG LEU F 269 " pdb=" CB LEU F 269 " pdb=" CD1 LEU F 269 " pdb=" CD2 LEU F 269 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.38e-01 ... (remaining 1723 not shown) Planarity restraints: 1758 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS E 190 " -0.010 2.00e-02 2.50e+03 1.45e-02 3.15e+00 pdb=" CG HIS E 190 " 0.030 2.00e-02 2.50e+03 pdb=" ND1 HIS E 190 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 HIS E 190 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 HIS E 190 " 0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS E 190 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 143 " -0.009 2.00e-02 2.50e+03 1.71e-02 2.92e+00 pdb=" C LEU C 143 " 0.030 2.00e-02 2.50e+03 pdb=" O LEU C 143 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG C 144 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 180 " 0.027 5.00e-02 4.00e+02 4.09e-02 2.67e+00 pdb=" N PRO C 181 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO C 181 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 181 " 0.023 5.00e-02 4.00e+02 ... (remaining 1755 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1127 2.75 - 3.29: 10426 3.29 - 3.82: 19078 3.82 - 4.36: 22169 4.36 - 4.90: 38034 Nonbonded interactions: 90834 Sorted by model distance: nonbonded pdb=" O LEU E 295 " pdb=" OH TYR E 309 " model vdw 2.209 3.040 nonbonded pdb=" OH TYR C 229 " pdb=" OD2 ASP C 275 " model vdw 2.213 3.040 nonbonded pdb=" OH TYR F 229 " pdb=" OD2 ASP F 275 " model vdw 2.229 3.040 nonbonded pdb=" OH TYR F 126 " pdb=" NH2 ARG F 150 " model vdw 2.231 3.120 nonbonded pdb=" O LEU B 295 " pdb=" OH TYR B 309 " model vdw 2.238 3.040 ... (remaining 90829 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = (chain 'B' and resid 20 through 283) selection = (chain 'C' and (resid 20 through 129 or resid 181 through 283)) selection = (chain 'E' and resid 20 through 283) selection = (chain 'F' and (resid 20 through 129 or resid 181 through 283)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 30.370 Find NCS groups from input model: 0.410 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: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 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 : 0.003 0.041 11052 Z= 0.200 Angle : 0.523 9.896 15196 Z= 0.279 Chirality : 0.039 0.249 1726 Planarity : 0.004 0.049 1758 Dihedral : 17.515 172.077 4240 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.24), residues: 1212 helix: 2.00 (0.21), residues: 572 sheet: -0.19 (0.39), residues: 186 loop : -0.96 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 44 HIS 0.019 0.002 HIS E 190 PHE 0.010 0.001 PHE A 89 TYR 0.025 0.001 TYR B 126 ARG 0.015 0.000 ARG F 150 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 1.158 Fit side-chains REVERT: B 24 PHE cc_start: 0.6987 (m-10) cc_final: 0.6238 (m-10) REVERT: C 120 ARG cc_start: 0.7736 (ttp-110) cc_final: 0.7200 (ttp-110) REVERT: C 140 MET cc_start: 0.8612 (mpp) cc_final: 0.7969 (mpp) REVERT: D 57 SER cc_start: 0.8830 (p) cc_final: 0.8535 (p) REVERT: F 146 HIS cc_start: 0.6869 (m90) cc_final: 0.5941 (m90) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.2578 time to fit residues: 68.2869 Evaluate side-chains 166 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 3.9990 chunk 95 optimal weight: 0.0370 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 0.1980 chunk 73 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN C 146 HIS D 48 GLN ** E 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11052 Z= 0.197 Angle : 0.533 10.743 15196 Z= 0.293 Chirality : 0.041 0.146 1726 Planarity : 0.004 0.042 1758 Dihedral : 18.261 177.610 1978 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.40 % Allowed : 7.72 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.24), residues: 1212 helix: 2.03 (0.21), residues: 582 sheet: 0.04 (0.40), residues: 182 loop : -0.86 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 44 HIS 0.011 0.001 HIS E 29 PHE 0.014 0.001 PHE C 212 TYR 0.011 0.001 TYR C 229 ARG 0.004 0.000 ARG D 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 182 time to evaluate : 1.038 Fit side-chains REVERT: B 24 PHE cc_start: 0.6825 (m-10) cc_final: 0.6615 (m-10) REVERT: B 40 THR cc_start: 0.8121 (m) cc_final: 0.7910 (m) REVERT: C 120 ARG cc_start: 0.7649 (ttp-110) cc_final: 0.7351 (ttp-110) REVERT: C 140 MET cc_start: 0.8724 (mpp) cc_final: 0.7995 (mpp) REVERT: C 147 GLU cc_start: 0.7120 (mp0) cc_final: 0.6347 (mp0) REVERT: D 9 LYS cc_start: 0.7967 (ptmm) cc_final: 0.7694 (ptmt) REVERT: D 57 SER cc_start: 0.8753 (p) cc_final: 0.8486 (p) REVERT: E 36 ASP cc_start: 0.7286 (p0) cc_final: 0.7061 (p0) REVERT: E 227 ASP cc_start: 0.8534 (OUTLIER) cc_final: 0.7921 (t70) REVERT: F 250 ASP cc_start: 0.8141 (t0) cc_final: 0.7938 (t0) outliers start: 14 outliers final: 11 residues processed: 189 average time/residue: 0.2315 time to fit residues: 61.7038 Evaluate side-chains 171 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 227 ASP Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 265 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 102 optimal weight: 0.4980 chunk 113 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 146 HIS D 48 GLN F 183 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11052 Z= 0.281 Angle : 0.543 8.167 15196 Z= 0.295 Chirality : 0.041 0.149 1726 Planarity : 0.004 0.040 1758 Dihedral : 18.354 173.209 1978 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.40 % Allowed : 10.92 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.24), residues: 1212 helix: 1.97 (0.21), residues: 582 sheet: -0.08 (0.39), residues: 182 loop : -0.94 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 83 HIS 0.013 0.001 HIS E 29 PHE 0.011 0.001 PHE A 89 TYR 0.012 0.001 TYR C 223 ARG 0.004 0.000 ARG D 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 1.199 Fit side-chains REVERT: B 40 THR cc_start: 0.8191 (m) cc_final: 0.7959 (m) REVERT: C 17 ARG cc_start: 0.7744 (mtm110) cc_final: 0.7430 (mtp-110) REVERT: C 20 ASP cc_start: 0.8367 (m-30) cc_final: 0.8033 (m-30) REVERT: C 140 MET cc_start: 0.8650 (mpp) cc_final: 0.7995 (mpp) REVERT: E 227 ASP cc_start: 0.8639 (OUTLIER) cc_final: 0.8124 (t70) outliers start: 24 outliers final: 18 residues processed: 176 average time/residue: 0.2444 time to fit residues: 60.1770 Evaluate side-chains 178 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 227 ASP Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 215 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 121 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 HIS D 48 GLN F 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11052 Z= 0.221 Angle : 0.519 12.004 15196 Z= 0.282 Chirality : 0.040 0.147 1726 Planarity : 0.003 0.039 1758 Dihedral : 18.315 173.306 1978 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.30 % Allowed : 13.13 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.24), residues: 1212 helix: 2.07 (0.21), residues: 582 sheet: -0.04 (0.40), residues: 182 loop : -0.91 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 83 HIS 0.009 0.001 HIS C 146 PHE 0.013 0.001 PHE F 176 TYR 0.010 0.001 TYR F 126 ARG 0.003 0.000 ARG C 120 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 1.170 Fit side-chains REVERT: B 40 THR cc_start: 0.8187 (m) cc_final: 0.7949 (m) REVERT: C 140 MET cc_start: 0.8494 (mpp) cc_final: 0.7900 (mpp) REVERT: D 9 LYS cc_start: 0.7940 (ptmm) cc_final: 0.7665 (ptmt) REVERT: F 250 ASP cc_start: 0.8175 (t0) cc_final: 0.7884 (t0) outliers start: 23 outliers final: 17 residues processed: 188 average time/residue: 0.2329 time to fit residues: 62.2818 Evaluate side-chains 179 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 215 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 1 optimal weight: 0.4980 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 109 optimal weight: 7.9990 chunk 30 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 HIS C 146 HIS D 48 GLN F 184 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11052 Z= 0.192 Angle : 0.502 7.685 15196 Z= 0.276 Chirality : 0.040 0.148 1726 Planarity : 0.003 0.037 1758 Dihedral : 18.250 172.916 1978 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.20 % Allowed : 15.93 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.24), residues: 1212 helix: 2.19 (0.21), residues: 582 sheet: -0.00 (0.39), residues: 182 loop : -0.87 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 83 HIS 0.008 0.001 HIS E 29 PHE 0.011 0.001 PHE D 89 TYR 0.010 0.001 TYR F 223 ARG 0.004 0.000 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 1.104 Fit side-chains REVERT: B 40 THR cc_start: 0.8191 (m) cc_final: 0.7950 (m) REVERT: C 140 MET cc_start: 0.8570 (mpp) cc_final: 0.7912 (mpp) REVERT: D 9 LYS cc_start: 0.7939 (ptmm) cc_final: 0.7673 (ptmt) REVERT: E 227 ASP cc_start: 0.8619 (OUTLIER) cc_final: 0.8145 (t70) REVERT: F 140 MET cc_start: 0.7694 (mmm) cc_final: 0.7394 (tpp) REVERT: F 261 ASP cc_start: 0.7756 (t0) cc_final: 0.7553 (t0) outliers start: 22 outliers final: 16 residues processed: 182 average time/residue: 0.2478 time to fit residues: 62.9881 Evaluate side-chains 176 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 217 HIS Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 227 ASP Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 215 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.0870 chunk 109 optimal weight: 8.9990 chunk 24 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 HIS C 146 HIS D 48 GLN F 184 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11052 Z= 0.226 Angle : 0.522 12.219 15196 Z= 0.283 Chirality : 0.040 0.179 1726 Planarity : 0.003 0.036 1758 Dihedral : 18.300 172.528 1978 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.71 % Allowed : 16.03 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.24), residues: 1212 helix: 2.15 (0.21), residues: 582 sheet: -0.05 (0.39), residues: 182 loop : -0.88 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 83 HIS 0.008 0.001 HIS E 29 PHE 0.017 0.001 PHE A 35 TYR 0.011 0.001 TYR C 223 ARG 0.005 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 1.189 Fit side-chains REVERT: B 40 THR cc_start: 0.8211 (m) cc_final: 0.7974 (m) REVERT: C 140 MET cc_start: 0.8581 (mpp) cc_final: 0.7923 (mpp) REVERT: D 9 LYS cc_start: 0.7950 (ptmm) cc_final: 0.7683 (ptmt) REVERT: E 227 ASP cc_start: 0.8605 (OUTLIER) cc_final: 0.8148 (t70) REVERT: F 140 MET cc_start: 0.7743 (mmm) cc_final: 0.7420 (tpp) REVERT: F 261 ASP cc_start: 0.7775 (t0) cc_final: 0.7571 (t0) outliers start: 27 outliers final: 17 residues processed: 177 average time/residue: 0.2445 time to fit residues: 60.7315 Evaluate side-chains 174 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 227 ASP Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 215 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 68 optimal weight: 0.0970 chunk 102 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 HIS C 146 HIS D 48 GLN E 190 HIS F 184 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11052 Z= 0.235 Angle : 0.523 7.695 15196 Z= 0.286 Chirality : 0.041 0.176 1726 Planarity : 0.003 0.035 1758 Dihedral : 18.317 172.405 1978 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.61 % Allowed : 17.23 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.24), residues: 1212 helix: 2.15 (0.21), residues: 582 sheet: -0.12 (0.39), residues: 182 loop : -0.92 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 83 HIS 0.013 0.001 HIS B 29 PHE 0.013 0.001 PHE A 35 TYR 0.010 0.001 TYR F 223 ARG 0.005 0.000 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 1.128 Fit side-chains REVERT: B 40 THR cc_start: 0.8227 (m) cc_final: 0.7981 (m) REVERT: C 140 MET cc_start: 0.8575 (mpp) cc_final: 0.7919 (mpp) REVERT: D 9 LYS cc_start: 0.7978 (ptmm) cc_final: 0.7693 (ptmt) REVERT: E 227 ASP cc_start: 0.8513 (OUTLIER) cc_final: 0.8039 (t70) REVERT: F 140 MET cc_start: 0.7721 (mmm) cc_final: 0.7396 (tpp) REVERT: F 261 ASP cc_start: 0.7779 (t0) cc_final: 0.7567 (t0) outliers start: 26 outliers final: 18 residues processed: 176 average time/residue: 0.2408 time to fit residues: 59.8402 Evaluate side-chains 170 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 227 ASP Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 215 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 0.0270 chunk 77 optimal weight: 0.6980 chunk 82 optimal weight: 0.2980 chunk 60 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 116 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 HIS C 146 HIS D 48 GLN F 184 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11052 Z= 0.180 Angle : 0.513 12.990 15196 Z= 0.279 Chirality : 0.040 0.188 1726 Planarity : 0.003 0.034 1758 Dihedral : 18.244 172.424 1978 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.30 % Allowed : 17.54 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.24), residues: 1212 helix: 2.21 (0.21), residues: 582 sheet: -0.09 (0.39), residues: 182 loop : -0.89 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 44 HIS 0.013 0.001 HIS B 29 PHE 0.011 0.001 PHE A 35 TYR 0.009 0.001 TYR F 223 ARG 0.005 0.000 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 1.193 Fit side-chains REVERT: B 40 THR cc_start: 0.8266 (m) cc_final: 0.7995 (m) REVERT: C 140 MET cc_start: 0.8564 (mpp) cc_final: 0.7917 (mpp) REVERT: D 9 LYS cc_start: 0.7956 (ptmm) cc_final: 0.7682 (ptmt) REVERT: F 140 MET cc_start: 0.7706 (mmm) cc_final: 0.7385 (tpp) REVERT: F 261 ASP cc_start: 0.7755 (t0) cc_final: 0.7548 (t0) outliers start: 23 outliers final: 18 residues processed: 172 average time/residue: 0.2483 time to fit residues: 59.7789 Evaluate side-chains 170 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 217 HIS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 215 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.6980 chunk 116 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 49 optimal weight: 10.0000 chunk 88 optimal weight: 0.4980 chunk 34 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 74 optimal weight: 0.2980 chunk 119 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 HIS C 146 HIS D 48 GLN F 184 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11052 Z= 0.185 Angle : 0.509 8.804 15196 Z= 0.278 Chirality : 0.040 0.202 1726 Planarity : 0.003 0.034 1758 Dihedral : 18.231 172.240 1978 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.30 % Allowed : 18.04 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.24), residues: 1212 helix: 2.24 (0.21), residues: 582 sheet: -0.09 (0.39), residues: 182 loop : -0.88 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 44 HIS 0.011 0.001 HIS B 29 PHE 0.019 0.001 PHE A 35 TYR 0.012 0.001 TYR C 126 ARG 0.007 0.000 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 1.220 Fit side-chains REVERT: B 40 THR cc_start: 0.8270 (m) cc_final: 0.8031 (m) REVERT: B 272 MET cc_start: 0.7495 (ttm) cc_final: 0.7232 (mtt) REVERT: C 140 MET cc_start: 0.8568 (mpp) cc_final: 0.7928 (mpp) REVERT: D 9 LYS cc_start: 0.7936 (ptmm) cc_final: 0.7672 (ptmt) REVERT: F 140 MET cc_start: 0.7703 (mmm) cc_final: 0.7377 (tpp) REVERT: F 261 ASP cc_start: 0.7769 (t0) cc_final: 0.7558 (t0) outliers start: 23 outliers final: 18 residues processed: 173 average time/residue: 0.2386 time to fit residues: 58.5764 Evaluate side-chains 172 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LYS Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 269 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 106 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 HIS C 146 HIS D 48 GLN F 184 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11052 Z= 0.219 Angle : 0.540 14.268 15196 Z= 0.287 Chirality : 0.041 0.196 1726 Planarity : 0.003 0.034 1758 Dihedral : 18.276 172.109 1978 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.90 % Allowed : 18.64 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.24), residues: 1212 helix: 2.21 (0.21), residues: 582 sheet: -0.12 (0.39), residues: 182 loop : -0.92 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 83 HIS 0.007 0.001 HIS E 29 PHE 0.018 0.001 PHE A 35 TYR 0.011 0.001 TYR F 126 ARG 0.008 0.000 ARG F 150 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 1.224 Fit side-chains REVERT: B 40 THR cc_start: 0.8267 (m) cc_final: 0.7994 (m) REVERT: C 140 MET cc_start: 0.8546 (mpp) cc_final: 0.7916 (mpp) REVERT: D 9 LYS cc_start: 0.7960 (ptmm) cc_final: 0.7668 (ptmt) REVERT: F 140 MET cc_start: 0.7699 (mmm) cc_final: 0.7396 (tpp) REVERT: F 261 ASP cc_start: 0.7781 (t0) cc_final: 0.7579 (t0) outliers start: 19 outliers final: 16 residues processed: 172 average time/residue: 0.2411 time to fit residues: 59.2392 Evaluate side-chains 167 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 190 HIS Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 215 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 102 optimal weight: 0.2980 chunk 12 optimal weight: 0.2980 chunk 18 optimal weight: 7.9990 chunk 87 optimal weight: 0.0980 chunk 5 optimal weight: 2.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 HIS D 48 GLN F 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.171787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.131620 restraints weight = 12432.095| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.23 r_work: 0.3501 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11052 Z= 0.164 Angle : 0.514 13.467 15196 Z= 0.277 Chirality : 0.040 0.205 1726 Planarity : 0.003 0.038 1758 Dihedral : 18.187 172.137 1978 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.90 % Allowed : 18.64 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.24), residues: 1212 helix: 2.31 (0.21), residues: 582 sheet: -0.05 (0.40), residues: 182 loop : -0.85 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 44 HIS 0.005 0.001 HIS E 29 PHE 0.017 0.001 PHE A 35 TYR 0.012 0.001 TYR F 126 ARG 0.009 0.000 ARG F 150 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2477.47 seconds wall clock time: 45 minutes 46.05 seconds (2746.05 seconds total)