Starting phenix.real_space_refine on Tue May 13 23:38:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fy9_29561/05_2025/8fy9_29561.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fy9_29561/05_2025/8fy9_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/cci-nas-00/data/ceres_data/8fy9_29561/05_2025/8fy9_29561.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fy9_29561/05_2025/8fy9_29561.map" model { file = "/net/cci-nas-00/data/ceres_data/8fy9_29561/05_2025/8fy9_29561.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fy9_29561/05_2025/8fy9_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 7.00, per 1000 atoms: 0.65 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: 3.75 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: 3.35 Time building geometry restraints manager: 3.19 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.000 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 29.270 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.090 ------------------------------------------------------------------------------- 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= 0.138 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 Details of bonding type rmsd hydrogen bonds : bond 0.15890 ( 553) hydrogen bonds : angle 6.28341 ( 1568) covalent geometry : bond 0.00313 (11052) covalent geometry : angle 0.52313 (15196) *********************** 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 : 1.245 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: 0.2711 time to fit residues: 72.4867 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 : 1.206 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.170262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.129374 restraints weight = 12374.899| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.22 r_work: 0.3476 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 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= 0.141 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 Details of bonding type rmsd hydrogen bonds : bond 0.04158 ( 553) hydrogen bonds : angle 4.44097 ( 1568) covalent geometry : bond 0.00311 (11052) covalent geometry : angle 0.53298 (15196) *********************** 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 : 1.214 Fit side-chains REVERT: B 24 PHE cc_start: 0.7039 (m-10) cc_final: 0.6790 (m-10) REVERT: C 120 ARG cc_start: 0.7799 (ttp-110) cc_final: 0.7473 (ttp-110) REVERT: C 140 MET cc_start: 0.8782 (mpp) cc_final: 0.8095 (mpp) REVERT: C 147 GLU cc_start: 0.7262 (mp0) cc_final: 0.6476 (mp0) REVERT: D 9 LYS cc_start: 0.8100 (ptmm) cc_final: 0.7817 (ptmt) REVERT: E 36 ASP cc_start: 0.7732 (p0) cc_final: 0.7517 (p0) REVERT: E 115 GLU cc_start: 0.5136 (tp30) cc_final: 0.4867 (tp30) REVERT: E 227 ASP cc_start: 0.8754 (OUTLIER) cc_final: 0.8100 (t70) REVERT: F 140 MET cc_start: 0.7734 (mmm) cc_final: 0.7434 (tpt) REVERT: F 250 ASP cc_start: 0.8351 (t0) cc_final: 0.8026 (t0) outliers start: 14 outliers final: 11 residues processed: 189 average time/residue: 0.2279 time to fit residues: 61.1908 Evaluate side-chains 170 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 158 time to evaluate : 1.082 ------------------------------------------------------------------------------- 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 52 optimal weight: 0.9990 chunk 25 optimal weight: 0.0170 chunk 121 optimal weight: 0.0000 chunk 34 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.5226 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.171126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.130559 restraints weight = 12491.796| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.24 r_work: 0.3476 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1503 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= 0.126 Angle : 0.495 7.599 15196 Z= 0.272 Chirality : 0.040 0.146 1726 Planarity : 0.003 0.038 1758 Dihedral : 18.179 173.135 1978 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.10 % Allowed : 10.72 % Favored : 87.17 % 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: 2.12 (0.21), residues: 582 sheet: 0.06 (0.40), residues: 182 loop : -0.84 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 83 HIS 0.009 0.001 HIS E 29 PHE 0.011 0.001 PHE D 89 TYR 0.011 0.001 TYR F 126 ARG 0.004 0.000 ARG D 63 Details of bonding type rmsd hydrogen bonds : bond 0.03540 ( 553) hydrogen bonds : angle 4.15545 ( 1568) covalent geometry : bond 0.00279 (11052) covalent geometry : angle 0.49518 (15196) *********************** 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 194 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 1.120 Fit side-chains REVERT: C 20 ASP cc_start: 0.8508 (m-30) cc_final: 0.8257 (m-30) REVERT: C 120 ARG cc_start: 0.7729 (ttp-110) cc_final: 0.7507 (ttp-110) REVERT: C 140 MET cc_start: 0.8566 (mpp) cc_final: 0.7971 (mpp) REVERT: C 147 GLU cc_start: 0.7127 (mt-10) cc_final: 0.6414 (mp0) REVERT: D 9 LYS cc_start: 0.8072 (ptmm) cc_final: 0.7798 (ptmt) REVERT: D 82 TYR cc_start: 0.7660 (m-80) cc_final: 0.7403 (m-80) REVERT: E 115 GLU cc_start: 0.4976 (tp30) cc_final: 0.4716 (tp30) REVERT: E 119 LEU cc_start: 0.7986 (tp) cc_final: 0.7778 (tp) REVERT: F 140 MET cc_start: 0.7778 (mmm) cc_final: 0.7441 (mmm) REVERT: F 146 HIS cc_start: 0.6743 (m170) cc_final: 0.6326 (m90) outliers start: 21 outliers final: 17 residues processed: 183 average time/residue: 0.2302 time to fit residues: 59.7840 Evaluate side-chains 180 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 80 ILE 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 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 D residue 57 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 66 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 47 optimal weight: 20.0000 chunk 41 optimal weight: 0.3980 chunk 19 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 64 optimal weight: 0.6980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 48 GLN F 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.167241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.125996 restraints weight = 12464.916| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.24 r_work: 0.3415 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11052 Z= 0.193 Angle : 0.543 11.803 15196 Z= 0.293 Chirality : 0.041 0.146 1726 Planarity : 0.003 0.038 1758 Dihedral : 18.320 173.037 1978 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.30 % Allowed : 13.73 % Favored : 83.97 % 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: 1.03 (0.24), residues: 1212 helix: 2.07 (0.21), residues: 582 sheet: -0.01 (0.40), residues: 182 loop : -0.89 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 83 HIS 0.012 0.002 HIS E 29 PHE 0.020 0.001 PHE F 176 TYR 0.011 0.001 TYR F 223 ARG 0.004 0.000 ARG D 63 Details of bonding type rmsd hydrogen bonds : bond 0.03735 ( 553) hydrogen bonds : angle 4.15220 ( 1568) covalent geometry : bond 0.00452 (11052) covalent geometry : angle 0.54317 (15196) *********************** 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 195 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 1.213 Fit side-chains REVERT: B 40 THR cc_start: 0.8299 (m) cc_final: 0.8099 (m) REVERT: C 120 ARG cc_start: 0.7648 (ttp-110) cc_final: 0.7439 (ttp-110) REVERT: C 140 MET cc_start: 0.8453 (mpp) cc_final: 0.7881 (mpp) REVERT: F 140 MET cc_start: 0.7720 (mmm) cc_final: 0.7352 (mmm) REVERT: F 146 HIS cc_start: 0.6683 (m170) cc_final: 0.6385 (m90) REVERT: F 176 PHE cc_start: 0.5397 (t80) cc_final: 0.5127 (t80) REVERT: F 250 ASP cc_start: 0.8319 (t0) cc_final: 0.7901 (t0) outliers start: 23 outliers final: 18 residues processed: 186 average time/residue: 0.2415 time to fit residues: 62.9643 Evaluate side-chains 183 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 1.218 ------------------------------------------------------------------------------- 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 D residue 57 SER 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 40 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 125 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 47 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 E 190 HIS F 184 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.168809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.128061 restraints weight = 12443.599| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.23 r_work: 0.3442 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.1746 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= 0.143 Angle : 0.502 7.493 15196 Z= 0.275 Chirality : 0.040 0.147 1726 Planarity : 0.003 0.036 1758 Dihedral : 18.278 172.863 1978 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.40 % Allowed : 15.33 % Favored : 82.26 % 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: 1.13 (0.24), residues: 1212 helix: 2.19 (0.21), residues: 582 sheet: -0.02 (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 0.009 0.001 HIS E 29 PHE 0.013 0.001 PHE F 176 TYR 0.011 0.001 TYR C 223 ARG 0.005 0.000 ARG C 150 Details of bonding type rmsd hydrogen bonds : bond 0.03381 ( 553) hydrogen bonds : angle 4.06548 ( 1568) covalent geometry : bond 0.00329 (11052) covalent geometry : angle 0.50185 (15196) *********************** 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 194 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 1.112 Fit side-chains REVERT: B 40 THR cc_start: 0.8290 (m) cc_final: 0.8049 (m) REVERT: C 140 MET cc_start: 0.8442 (mpp) cc_final: 0.7865 (mpp) REVERT: D 9 LYS cc_start: 0.8064 (ptmm) cc_final: 0.7757 (ptmt) REVERT: E 115 GLU cc_start: 0.4980 (tp30) cc_final: 0.4746 (tp30) REVERT: F 140 MET cc_start: 0.7731 (mmm) cc_final: 0.7353 (mmm) REVERT: F 146 HIS cc_start: 0.6752 (m170) cc_final: 0.6469 (m90) REVERT: F 250 ASP cc_start: 0.8309 (t0) cc_final: 0.7931 (t0) outliers start: 24 outliers final: 18 residues processed: 185 average time/residue: 0.2360 time to fit residues: 61.6462 Evaluate side-chains 177 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 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 D residue 57 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 120 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 97 optimal weight: 0.4980 chunk 83 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 69 optimal weight: 0.0050 chunk 110 optimal weight: 5.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.169815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.129376 restraints weight = 12518.609| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.24 r_work: 0.3462 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1871 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= 0.127 Angle : 0.501 12.603 15196 Z= 0.271 Chirality : 0.040 0.164 1726 Planarity : 0.003 0.034 1758 Dihedral : 18.228 172.499 1978 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.10 % Allowed : 16.23 % Favored : 81.66 % 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: 1.18 (0.24), residues: 1212 helix: 2.24 (0.21), residues: 582 sheet: -0.03 (0.39), residues: 182 loop : -0.83 (0.28), 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 0.011 0.001 PHE A 35 TYR 0.010 0.001 TYR B 26 ARG 0.006 0.000 ARG C 120 Details of bonding type rmsd hydrogen bonds : bond 0.03240 ( 553) hydrogen bonds : angle 4.00309 ( 1568) covalent geometry : bond 0.00287 (11052) covalent geometry : angle 0.50112 (15196) *********************** 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: 21 poor density : 166 time to evaluate : 1.103 Fit side-chains REVERT: B 40 THR cc_start: 0.8256 (m) cc_final: 0.8007 (m) REVERT: C 140 MET cc_start: 0.8438 (mpp) cc_final: 0.7827 (mpp) REVERT: D 9 LYS cc_start: 0.8067 (ptmm) cc_final: 0.7766 (ptmt) REVERT: E 115 GLU cc_start: 0.4986 (tp30) cc_final: 0.4747 (tp30) REVERT: F 140 MET cc_start: 0.7735 (mmm) cc_final: 0.7356 (mmm) REVERT: F 250 ASP cc_start: 0.8316 (t0) cc_final: 0.7950 (t0) outliers start: 21 outliers final: 16 residues processed: 179 average time/residue: 0.2336 time to fit residues: 58.7075 Evaluate side-chains 176 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 1.068 ------------------------------------------------------------------------------- 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 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 35 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 50 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.165660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.124686 restraints weight = 12780.116| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.23 r_work: 0.3395 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 11052 Z= 0.206 Angle : 0.556 7.949 15196 Z= 0.300 Chirality : 0.042 0.209 1726 Planarity : 0.004 0.033 1758 Dihedral : 18.425 172.276 1978 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.81 % Allowed : 16.33 % Favored : 80.86 % 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: 0.94 (0.24), residues: 1212 helix: 2.06 (0.21), residues: 582 sheet: -0.19 (0.39), residues: 182 loop : -0.94 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 83 HIS 0.012 0.001 HIS E 29 PHE 0.019 0.002 PHE A 35 TYR 0.013 0.002 TYR C 223 ARG 0.007 0.000 ARG C 120 Details of bonding type rmsd hydrogen bonds : bond 0.03723 ( 553) hydrogen bonds : angle 4.11948 ( 1568) covalent geometry : bond 0.00488 (11052) covalent geometry : angle 0.55645 (15196) *********************** 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 190 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 1.077 Fit side-chains REVERT: B 40 THR cc_start: 0.8309 (m) cc_final: 0.8062 (m) REVERT: B 250 ASP cc_start: 0.7604 (t70) cc_final: 0.7374 (t70) REVERT: C 140 MET cc_start: 0.8433 (mpp) cc_final: 0.7800 (mpp) REVERT: D 9 LYS cc_start: 0.8085 (ptmm) cc_final: 0.7762 (ptmt) REVERT: E 115 GLU cc_start: 0.5086 (tp30) cc_final: 0.4838 (tp30) REVERT: F 140 MET cc_start: 0.7737 (mmm) cc_final: 0.7347 (mmm) outliers start: 28 outliers final: 20 residues processed: 181 average time/residue: 0.2238 time to fit residues: 57.5738 Evaluate side-chains 174 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 1.181 ------------------------------------------------------------------------------- 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 55 GLU 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 190 HIS Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 232 GLU 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 110 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 C 183 ASN D 48 GLN F 184 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.168897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.128207 restraints weight = 12565.962| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.25 r_work: 0.3445 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1968 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= 0.137 Angle : 0.528 13.946 15196 Z= 0.282 Chirality : 0.040 0.182 1726 Planarity : 0.003 0.033 1758 Dihedral : 18.261 172.120 1978 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.40 % Allowed : 16.93 % Favored : 80.66 % 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: 1.08 (0.24), residues: 1212 helix: 2.17 (0.21), residues: 582 sheet: -0.18 (0.39), residues: 182 loop : -0.86 (0.28), 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 0.014 0.001 PHE A 35 TYR 0.011 0.001 TYR C 126 ARG 0.006 0.000 ARG D 63 Details of bonding type rmsd hydrogen bonds : bond 0.03316 ( 553) hydrogen bonds : angle 4.05036 ( 1568) covalent geometry : bond 0.00314 (11052) covalent geometry : angle 0.52838 (15196) *********************** 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 182 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 1.258 Fit side-chains REVERT: B 40 THR cc_start: 0.8332 (m) cc_final: 0.8075 (m) REVERT: B 250 ASP cc_start: 0.7569 (t70) cc_final: 0.7349 (t70) REVERT: C 140 MET cc_start: 0.8330 (mpp) cc_final: 0.7736 (mpp) REVERT: C 223 TYR cc_start: 0.7522 (m-80) cc_final: 0.7261 (m-80) REVERT: C 227 ASP cc_start: 0.8012 (m-30) cc_final: 0.7760 (m-30) REVERT: D 9 LYS cc_start: 0.8091 (ptmm) cc_final: 0.7773 (ptmt) REVERT: E 115 GLU cc_start: 0.4930 (tp30) cc_final: 0.4697 (tp30) REVERT: E 251 ILE cc_start: 0.8646 (mm) cc_final: 0.8375 (mm) REVERT: F 140 MET cc_start: 0.7734 (mmm) cc_final: 0.7345 (mmm) outliers start: 24 outliers final: 19 residues processed: 174 average time/residue: 0.2410 time to fit residues: 58.6171 Evaluate side-chains 168 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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 50 ILE 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 190 HIS Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 232 GLU 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 109 optimal weight: 0.4980 chunk 73 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 75 optimal weight: 0.5980 chunk 99 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 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 C 183 ASN D 48 GLN F 184 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.169268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.128671 restraints weight = 12650.928| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.25 r_work: 0.3450 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2015 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= 0.134 Angle : 0.522 13.716 15196 Z= 0.281 Chirality : 0.040 0.178 1726 Planarity : 0.003 0.034 1758 Dihedral : 18.245 172.066 1978 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.51 % Allowed : 17.33 % 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: 1.13 (0.24), residues: 1212 helix: 2.21 (0.21), residues: 582 sheet: -0.16 (0.40), residues: 182 loop : -0.82 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 83 HIS 0.009 0.001 HIS B 29 PHE 0.013 0.001 PHE A 35 TYR 0.012 0.001 TYR C 126 ARG 0.008 0.000 ARG D 63 Details of bonding type rmsd hydrogen bonds : bond 0.03264 ( 553) hydrogen bonds : angle 4.01821 ( 1568) covalent geometry : bond 0.00308 (11052) covalent geometry : angle 0.52228 (15196) *********************** 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 181 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 1.077 Fit side-chains REVERT: B 40 THR cc_start: 0.8318 (m) cc_final: 0.8086 (m) REVERT: B 250 ASP cc_start: 0.7537 (t70) cc_final: 0.7127 (t0) REVERT: B 253 GLN cc_start: 0.8414 (tp40) cc_final: 0.8126 (tp40) REVERT: C 140 MET cc_start: 0.8465 (mpp) cc_final: 0.7853 (mpp) REVERT: C 223 TYR cc_start: 0.7474 (m-80) cc_final: 0.7219 (m-80) REVERT: C 227 ASP cc_start: 0.8051 (m-30) cc_final: 0.7780 (m-30) REVERT: D 9 LYS cc_start: 0.8065 (ptmm) cc_final: 0.7779 (ptmt) REVERT: E 115 GLU cc_start: 0.5033 (tp30) cc_final: 0.4770 (tp30) REVERT: E 251 ILE cc_start: 0.8670 (mm) cc_final: 0.8407 (mm) REVERT: F 140 MET cc_start: 0.7725 (mmm) cc_final: 0.7332 (mmm) outliers start: 25 outliers final: 21 residues processed: 173 average time/residue: 0.2442 time to fit residues: 59.8925 Evaluate side-chains 176 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 1.192 ------------------------------------------------------------------------------- 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 50 ILE 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 D residue 57 SER 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 E residue 232 GLU 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 42 optimal weight: 0.1980 chunk 53 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 87 optimal weight: 0.1980 chunk 18 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- 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 C 183 ASN D 48 GLN F 184 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.169770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.129391 restraints weight = 12613.156| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.25 r_work: 0.3475 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2068 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= 0.129 Angle : 0.514 10.357 15196 Z= 0.280 Chirality : 0.040 0.189 1726 Planarity : 0.003 0.036 1758 Dihedral : 18.237 172.054 1978 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.51 % Allowed : 17.23 % Favored : 80.26 % 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: 1.16 (0.24), residues: 1212 helix: 2.25 (0.21), residues: 582 sheet: -0.13 (0.40), residues: 182 loop : -0.84 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 83 HIS 0.009 0.001 HIS B 29 PHE 0.013 0.001 PHE C 212 TYR 0.010 0.001 TYR F 126 ARG 0.008 0.000 ARG D 63 Details of bonding type rmsd hydrogen bonds : bond 0.03238 ( 553) hydrogen bonds : angle 4.02353 ( 1568) covalent geometry : bond 0.00293 (11052) covalent geometry : angle 0.51389 (15196) ********************** 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 186 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 1.068 Fit side-chains REVERT: B 40 THR cc_start: 0.8437 (m) cc_final: 0.8181 (m) REVERT: B 250 ASP cc_start: 0.7464 (t70) cc_final: 0.7055 (t0) REVERT: B 253 GLN cc_start: 0.8434 (tp40) cc_final: 0.8168 (tp40) REVERT: C 140 MET cc_start: 0.8294 (mpp) cc_final: 0.7700 (mpp) REVERT: C 223 TYR cc_start: 0.7583 (m-80) cc_final: 0.7312 (m-80) REVERT: C 227 ASP cc_start: 0.8155 (m-30) cc_final: 0.7915 (m-30) REVERT: C 276 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7864 (mp) REVERT: D 9 LYS cc_start: 0.8079 (ptmm) cc_final: 0.7795 (ptmt) REVERT: E 115 GLU cc_start: 0.5051 (tp30) cc_final: 0.4779 (tp30) REVERT: E 251 ILE cc_start: 0.8728 (mm) cc_final: 0.8484 (mm) REVERT: F 140 MET cc_start: 0.7697 (mmm) cc_final: 0.7296 (mmm) REVERT: F 150 ARG cc_start: 0.7777 (ptp-170) cc_final: 0.7573 (ptp-170) REVERT: F 250 ASP cc_start: 0.8377 (t0) cc_final: 0.7882 (t0) outliers start: 25 outliers final: 22 residues processed: 177 average time/residue: 0.2304 time to fit residues: 58.0520 Evaluate side-chains 175 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 1.119 ------------------------------------------------------------------------------- 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 50 ILE 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 C residue 276 LEU Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain E residue 71 VAL 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 E residue 232 GLU 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 60 optimal weight: 0.9990 chunk 28 optimal weight: 0.0040 chunk 104 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 125 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 79 optimal weight: 0.0040 chunk 2 optimal weight: 2.9990 overall best weight: 0.6008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 HIS C 183 ASN D 48 GLN F 184 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.170033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.129702 restraints weight = 12442.614| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.23 r_work: 0.3461 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2112 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= 0.131 Angle : 0.526 13.773 15196 Z= 0.284 Chirality : 0.040 0.183 1726 Planarity : 0.003 0.036 1758 Dihedral : 18.252 171.998 1978 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.10 % Allowed : 17.84 % Favored : 80.06 % 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: 1.16 (0.24), residues: 1212 helix: 2.24 (0.21), residues: 582 sheet: -0.11 (0.40), residues: 182 loop : -0.84 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 83 HIS 0.013 0.001 HIS B 29 PHE 0.012 0.001 PHE A 35 TYR 0.013 0.001 TYR B 26 ARG 0.008 0.000 ARG D 63 Details of bonding type rmsd hydrogen bonds : bond 0.03253 ( 553) hydrogen bonds : angle 4.03265 ( 1568) covalent geometry : bond 0.00297 (11052) covalent geometry : angle 0.52587 (15196) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5231.85 seconds wall clock time: 91 minutes 15.98 seconds (5475.98 seconds total)