Starting phenix.real_space_refine on Thu Jul 31 08:28:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e87_31011/07_2025/7e87_31011.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e87_31011/07_2025/7e87_31011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7e87_31011/07_2025/7e87_31011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e87_31011/07_2025/7e87_31011.map" model { file = "/net/cci-nas-00/data/ceres_data/7e87_31011/07_2025/7e87_31011.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e87_31011/07_2025/7e87_31011.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 8642 2.51 5 N 2242 2.21 5 O 2350 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13304 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 3122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3122 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 14, 'TRANS': 373} Chain breaks: 2 Chain: "A" Number of atoms: 3120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3120 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 14, 'TRANS': 373} Chain breaks: 2 Chain: "J" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 205 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "I" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 205 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "C" Number of atoms: 3122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3122 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 14, 'TRANS': 373} Chain breaks: 2 Chain: "D" Number of atoms: 3120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3120 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 14, 'TRANS': 373} Chain breaks: 2 Chain: "E" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 205 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "F" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 205 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Time building chain proxies: 8.56, per 1000 atoms: 0.64 Number of scatterers: 13304 At special positions: 0 Unit cell: (109, 111, 129, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 2350 8.00 N 2242 7.00 C 8642 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: 3.36 Conformation dependent library (CDL) restraints added in 1.8 seconds 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3160 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 4 sheets defined 73.0% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 70 through 76 removed outlier: 3.718A pdb=" N PHE B 74 " --> pdb=" O SER B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 102 removed outlier: 3.573A pdb=" N HIS B 94 " --> pdb=" O ASP B 90 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR B 99 " --> pdb=" O ILE B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 122 removed outlier: 3.618A pdb=" N PHE B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 147 removed outlier: 3.976A pdb=" N ARG B 147 " --> pdb=" O GLU B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 154 Processing helix chain 'B' and resid 168 through 177 Processing helix chain 'B' and resid 181 through 205 Processing helix chain 'B' and resid 228 through 250 Processing helix chain 'B' and resid 253 through 259 Processing helix chain 'B' and resid 260 through 282 Proline residue: B 272 - end of helix Processing helix chain 'B' and resid 288 through 296 Processing helix chain 'B' and resid 297 through 305 removed outlier: 3.542A pdb=" N ARG B 305 " --> pdb=" O LYS B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 319 Processing helix chain 'B' and resid 320 through 347 Processing helix chain 'B' and resid 356 through 369 Processing helix chain 'B' and resid 380 through 400 Processing helix chain 'B' and resid 401 through 434 removed outlier: 3.990A pdb=" N ASP B 420 " --> pdb=" O ASN B 416 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LYS B 421 " --> pdb=" O GLN B 417 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG B 434 " --> pdb=" O LEU B 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 88 through 101 removed outlier: 3.661A pdb=" N PHE A 92 " --> pdb=" O ASP A 88 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG A 93 " --> pdb=" O PRO A 89 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N HIS A 94 " --> pdb=" O ASP A 90 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE A 95 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR A 99 " --> pdb=" O ILE A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 123 Processing helix chain 'A' and resid 125 through 129 removed outlier: 3.603A pdb=" N ILE A 128 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 129 " --> pdb=" O PRO A 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 125 through 129' Processing helix chain 'A' and resid 131 through 150 removed outlier: 3.508A pdb=" N ARG A 147 " --> pdb=" O GLU A 143 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 148 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASP A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 153 No H-bonds generated for 'chain 'A' and resid 151 through 153' Processing helix chain 'A' and resid 167 through 177 removed outlier: 3.690A pdb=" N ASN A 177 " --> pdb=" O ARG A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 205 Processing helix chain 'A' and resid 228 through 250 removed outlier: 4.462A pdb=" N ILE A 239 " --> pdb=" O ALA A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 260 Processing helix chain 'A' and resid 260 through 282 Proline residue: A 272 - end of helix Processing helix chain 'A' and resid 288 through 295 removed outlier: 3.709A pdb=" N PHE A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 305 removed outlier: 3.978A pdb=" N ARG A 299 " --> pdb=" O ARG A 296 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS A 302 " --> pdb=" O ARG A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 320 Processing helix chain 'A' and resid 320 through 346 Processing helix chain 'A' and resid 356 through 369 Processing helix chain 'A' and resid 380 through 400 Processing helix chain 'A' and resid 401 through 434 Processing helix chain 'J' and resid 32 through 56 removed outlier: 3.509A pdb=" N ILE J 36 " --> pdb=" O LYS J 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 56 Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 70 through 76 removed outlier: 3.717A pdb=" N PHE C 74 " --> pdb=" O SER C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 102 removed outlier: 3.573A pdb=" N HIS C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR C 99 " --> pdb=" O ILE C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 122 removed outlier: 3.618A pdb=" N PHE C 122 " --> pdb=" O GLU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 147 removed outlier: 3.976A pdb=" N ARG C 147 " --> pdb=" O GLU C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 154 Processing helix chain 'C' and resid 168 through 177 Processing helix chain 'C' and resid 181 through 205 Processing helix chain 'C' and resid 228 through 250 Processing helix chain 'C' and resid 253 through 259 Processing helix chain 'C' and resid 260 through 282 Proline residue: C 272 - end of helix Processing helix chain 'C' and resid 288 through 296 Processing helix chain 'C' and resid 297 through 305 removed outlier: 3.542A pdb=" N ARG C 305 " --> pdb=" O LYS C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 319 Processing helix chain 'C' and resid 320 through 347 Processing helix chain 'C' and resid 356 through 369 Processing helix chain 'C' and resid 380 through 400 Processing helix chain 'C' and resid 401 through 434 removed outlier: 3.989A pdb=" N ASP C 420 " --> pdb=" O ASN C 416 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LYS C 421 " --> pdb=" O GLN C 417 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG C 434 " --> pdb=" O LEU C 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 70 through 75 Processing helix chain 'D' and resid 88 through 101 removed outlier: 3.661A pdb=" N PHE D 92 " --> pdb=" O ASP D 88 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG D 93 " --> pdb=" O PRO D 89 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N HIS D 94 " --> pdb=" O ASP D 90 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE D 95 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR D 99 " --> pdb=" O ILE D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 123 Processing helix chain 'D' and resid 125 through 129 removed outlier: 3.603A pdb=" N ILE D 128 " --> pdb=" O ILE D 125 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE D 129 " --> pdb=" O PRO D 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 125 through 129' Processing helix chain 'D' and resid 131 through 150 removed outlier: 3.506A pdb=" N ARG D 147 " --> pdb=" O GLU D 143 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU D 148 " --> pdb=" O ASN D 144 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASP D 150 " --> pdb=" O GLU D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 153 No H-bonds generated for 'chain 'D' and resid 151 through 153' Processing helix chain 'D' and resid 167 through 177 removed outlier: 3.690A pdb=" N ASN D 177 " --> pdb=" O ARG D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 205 Processing helix chain 'D' and resid 228 through 250 removed outlier: 4.463A pdb=" N ILE D 239 " --> pdb=" O ALA D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 260 Processing helix chain 'D' and resid 260 through 282 Proline residue: D 272 - end of helix Processing helix chain 'D' and resid 288 through 295 removed outlier: 3.708A pdb=" N PHE D 295 " --> pdb=" O THR D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 305 removed outlier: 3.978A pdb=" N ARG D 299 " --> pdb=" O ARG D 296 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS D 302 " --> pdb=" O ARG D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 320 Processing helix chain 'D' and resid 320 through 346 Processing helix chain 'D' and resid 356 through 369 Processing helix chain 'D' and resid 380 through 400 Processing helix chain 'D' and resid 401 through 434 Processing helix chain 'E' and resid 32 through 56 removed outlier: 3.509A pdb=" N ILE E 36 " --> pdb=" O LYS E 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 56 Processing sheet with id=AA1, first strand: chain 'B' and resid 51 through 55 Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.803A pdb=" N THR A 54 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE A 43 " --> pdb=" O THR A 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 51 through 55 Processing sheet with id=AA4, first strand: chain 'D' and resid 51 through 54 removed outlier: 3.802A pdb=" N THR D 54 " --> pdb=" O ILE D 43 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE D 43 " --> pdb=" O THR D 54 " (cutoff:3.500A) 868 hydrogen bonds defined for protein. 2532 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.87 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2917 1.33 - 1.45: 3108 1.45 - 1.57: 7483 1.57 - 1.69: 0 1.69 - 1.81: 104 Bond restraints: 13612 Sorted by residual: bond pdb=" C LEU C 400 " pdb=" N PRO C 401 " ideal model delta sigma weight residual 1.332 1.354 -0.022 8.20e-03 1.49e+04 7.08e+00 bond pdb=" C LEU B 400 " pdb=" N PRO B 401 " ideal model delta sigma weight residual 1.332 1.353 -0.021 8.20e-03 1.49e+04 6.60e+00 bond pdb=" C THR I 56 " pdb=" N PRO I 57 " ideal model delta sigma weight residual 1.334 1.350 -0.016 8.40e-03 1.42e+04 3.68e+00 bond pdb=" C THR F 56 " pdb=" N PRO F 57 " ideal model delta sigma weight residual 1.334 1.350 -0.016 8.40e-03 1.42e+04 3.68e+00 bond pdb=" CG LEU C 271 " pdb=" CD1 LEU C 271 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.79e+00 ... (remaining 13607 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 18001 1.71 - 3.43: 345 3.43 - 5.14: 81 5.14 - 6.86: 17 6.86 - 8.57: 10 Bond angle restraints: 18454 Sorted by residual: angle pdb=" N GLN A 417 " pdb=" CA GLN A 417 " pdb=" CB GLN A 417 " ideal model delta sigma weight residual 110.28 116.69 -6.41 1.55e+00 4.16e-01 1.71e+01 angle pdb=" N GLN D 417 " pdb=" CA GLN D 417 " pdb=" CB GLN D 417 " ideal model delta sigma weight residual 110.28 116.65 -6.37 1.55e+00 4.16e-01 1.69e+01 angle pdb=" N ILE B 112 " pdb=" CA ILE B 112 " pdb=" C ILE B 112 " ideal model delta sigma weight residual 112.12 109.32 2.80 8.40e-01 1.42e+00 1.11e+01 angle pdb=" N ILE C 112 " pdb=" CA ILE C 112 " pdb=" C ILE C 112 " ideal model delta sigma weight residual 112.12 109.36 2.76 8.40e-01 1.42e+00 1.08e+01 angle pdb=" N LEU A 271 " pdb=" CA LEU A 271 " pdb=" C LEU A 271 " ideal model delta sigma weight residual 109.81 116.98 -7.17 2.21e+00 2.05e-01 1.05e+01 ... (remaining 18449 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.05: 7091 16.05 - 32.10: 749 32.10 - 48.15: 168 48.15 - 64.20: 26 64.20 - 80.25: 8 Dihedral angle restraints: 8042 sinusoidal: 3154 harmonic: 4888 Sorted by residual: dihedral pdb=" CA VAL D 297 " pdb=" C VAL D 297 " pdb=" N PHE D 298 " pdb=" CA PHE D 298 " ideal model delta harmonic sigma weight residual 180.00 157.28 22.72 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA VAL A 297 " pdb=" C VAL A 297 " pdb=" N PHE A 298 " pdb=" CA PHE A 298 " ideal model delta harmonic sigma weight residual 180.00 157.29 22.71 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA PRO B 89 " pdb=" C PRO B 89 " pdb=" N ASP B 90 " pdb=" CA ASP B 90 " ideal model delta harmonic sigma weight residual 180.00 163.17 16.83 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 8039 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1448 0.040 - 0.080: 511 0.080 - 0.119: 138 0.119 - 0.159: 11 0.159 - 0.199: 8 Chirality restraints: 2116 Sorted by residual: chirality pdb=" CA LEU C 271 " pdb=" N LEU C 271 " pdb=" C LEU C 271 " pdb=" CB LEU C 271 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.89e-01 chirality pdb=" CA LEU A 271 " pdb=" N LEU A 271 " pdb=" C LEU A 271 " pdb=" CB LEU A 271 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.79e-01 chirality pdb=" CA LEU B 271 " pdb=" N LEU B 271 " pdb=" C LEU B 271 " pdb=" CB LEU B 271 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.75e-01 ... (remaining 2113 not shown) Planarity restraints: 2306 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 235 " -0.008 2.00e-02 2.50e+03 1.67e-02 2.80e+00 pdb=" C ALA C 235 " 0.029 2.00e-02 2.50e+03 pdb=" O ALA C 235 " -0.011 2.00e-02 2.50e+03 pdb=" N CYS C 236 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 235 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.74e+00 pdb=" C ALA B 235 " -0.029 2.00e-02 2.50e+03 pdb=" O ALA B 235 " 0.011 2.00e-02 2.50e+03 pdb=" N CYS B 236 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 238 " 0.008 2.00e-02 2.50e+03 1.57e-02 2.48e+00 pdb=" C MET C 238 " -0.027 2.00e-02 2.50e+03 pdb=" O MET C 238 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE C 239 " 0.009 2.00e-02 2.50e+03 ... (remaining 2303 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 268 2.67 - 3.23: 14220 3.23 - 3.78: 21300 3.78 - 4.34: 27696 4.34 - 4.90: 44582 Nonbonded interactions: 108066 Sorted by model distance: nonbonded pdb=" OG SER A 69 " pdb=" OE1 GLU A 71 " model vdw 2.111 3.040 nonbonded pdb=" OG SER D 69 " pdb=" OE1 GLU D 71 " model vdw 2.112 3.040 nonbonded pdb=" OD1 ASN C 97 " pdb=" NH1 ARG C 100 " model vdw 2.150 3.120 nonbonded pdb=" OD1 ASN B 97 " pdb=" NH1 ARG B 100 " model vdw 2.150 3.120 nonbonded pdb=" O MET A 238 " pdb=" OG1 THR A 241 " model vdw 2.174 3.040 ... (remaining 108061 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: 0.06 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 40 through 158 or resid 167 through 436)) selection = (chain 'B' and (resid 40 through 158 or resid 167 through 436)) selection = (chain 'C' and (resid 40 through 158 or resid 167 through 436)) selection = (chain 'D' and (resid 40 through 158 or resid 167 through 436)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' } 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: 3.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 32.500 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.060 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 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 0.044 13612 Z= 0.161 Angle : 0.648 8.571 18454 Z= 0.345 Chirality : 0.044 0.199 2116 Planarity : 0.005 0.039 2306 Dihedral : 13.861 80.250 4882 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: -0.03 (0.21), residues: 1632 helix: 0.84 (0.15), residues: 1128 sheet: None (None), residues: 0 loop : -1.98 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 31 HIS 0.004 0.001 HIS D 306 PHE 0.017 0.002 PHE D 187 TYR 0.019 0.001 TYR A 83 ARG 0.008 0.000 ARG D 142 Details of bonding type rmsd hydrogen bonds : bond 0.13336 ( 868) hydrogen bonds : angle 5.45668 ( 2532) covalent geometry : bond 0.00343 (13612) covalent geometry : angle 0.64819 (18454) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 418 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 ASN cc_start: 0.8210 (t0) cc_final: 0.7790 (t0) REVERT: B 98 PHE cc_start: 0.8324 (t80) cc_final: 0.7862 (t80) REVERT: B 110 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7403 (mm-30) REVERT: B 224 ARG cc_start: 0.4502 (pmt170) cc_final: 0.4296 (ptm160) REVERT: B 238 MET cc_start: 0.8048 (mmp) cc_final: 0.7808 (mmp) REVERT: B 308 GLN cc_start: 0.7033 (pm20) cc_final: 0.6823 (pm20) REVERT: B 315 TYR cc_start: 0.7165 (m-10) cc_final: 0.6844 (m-10) REVERT: B 318 LYS cc_start: 0.7209 (mptt) cc_final: 0.6870 (mptt) REVERT: B 418 ARG cc_start: 0.6524 (ptm-80) cc_final: 0.6301 (ptt90) REVERT: A 53 GLN cc_start: 0.7820 (mp10) cc_final: 0.7582 (mp10) REVERT: A 66 LEU cc_start: 0.7587 (tt) cc_final: 0.7168 (tt) REVERT: A 71 GLU cc_start: 0.7421 (mp0) cc_final: 0.7108 (mp0) REVERT: A 81 GLN cc_start: 0.6461 (mp10) cc_final: 0.5839 (mp10) REVERT: A 136 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7723 (tm-30) REVERT: A 138 LYS cc_start: 0.8117 (mmmt) cc_final: 0.7851 (mmmm) REVERT: A 149 GLN cc_start: 0.6885 (pp30) cc_final: 0.6603 (pp30) REVERT: A 170 ARG cc_start: 0.6707 (tpp-160) cc_final: 0.5860 (tpt170) REVERT: A 172 TRP cc_start: 0.7246 (t60) cc_final: 0.6794 (t60) REVERT: A 176 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7550 (tm-30) REVERT: A 312 ILE cc_start: 0.8604 (mt) cc_final: 0.8326 (mt) REVERT: C 97 ASN cc_start: 0.8216 (t0) cc_final: 0.7791 (t0) REVERT: C 98 PHE cc_start: 0.8331 (t80) cc_final: 0.7870 (t80) REVERT: C 110 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7404 (mm-30) REVERT: C 224 ARG cc_start: 0.4517 (pmt170) cc_final: 0.4299 (ptm160) REVERT: C 238 MET cc_start: 0.8047 (mmp) cc_final: 0.7806 (mmp) REVERT: C 308 GLN cc_start: 0.7034 (pm20) cc_final: 0.6825 (pm20) REVERT: C 315 TYR cc_start: 0.7102 (m-10) cc_final: 0.6797 (m-10) REVERT: C 318 LYS cc_start: 0.7210 (mptt) cc_final: 0.6873 (mptt) REVERT: C 418 ARG cc_start: 0.6519 (ptm-80) cc_final: 0.6298 (ptt90) REVERT: D 53 GLN cc_start: 0.7817 (mp10) cc_final: 0.7578 (mp10) REVERT: D 66 LEU cc_start: 0.7581 (tt) cc_final: 0.7162 (tt) REVERT: D 71 GLU cc_start: 0.7426 (mp0) cc_final: 0.7115 (mp0) REVERT: D 81 GLN cc_start: 0.6462 (mp10) cc_final: 0.5735 (mp10) REVERT: D 136 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7728 (tm-30) REVERT: D 138 LYS cc_start: 0.8119 (mmmt) cc_final: 0.7846 (mmmm) REVERT: D 149 GLN cc_start: 0.6883 (pp30) cc_final: 0.6602 (pp30) REVERT: D 170 ARG cc_start: 0.6706 (tpp-160) cc_final: 0.5857 (tpt170) REVERT: D 172 TRP cc_start: 0.7246 (t60) cc_final: 0.6749 (t60) REVERT: D 176 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7545 (tm-30) REVERT: D 312 ILE cc_start: 0.8600 (mt) cc_final: 0.8316 (mt) outliers start: 0 outliers final: 0 residues processed: 418 average time/residue: 0.2786 time to fit residues: 162.4499 Evaluate side-chains 273 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.5980 chunk 121 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 HIS B 105 HIS B 144 ASN B 408 ASN A 82 GLN ** A 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 HIS C 105 HIS C 144 ASN C 408 ASN ** D 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.142933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.094810 restraints weight = 27264.855| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.53 r_work: 0.3137 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 13612 Z= 0.254 Angle : 0.738 8.489 18454 Z= 0.394 Chirality : 0.048 0.188 2116 Planarity : 0.006 0.052 2306 Dihedral : 4.340 17.803 1852 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.09 % Allowed : 12.92 % Favored : 84.99 % 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: -0.08 (0.21), residues: 1632 helix: 0.88 (0.15), residues: 1144 sheet: None (None), residues: 0 loop : -2.34 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 362 HIS 0.009 0.002 HIS B 306 PHE 0.030 0.003 PHE D 194 TYR 0.022 0.002 TYR C 188 ARG 0.005 0.001 ARG B 87 Details of bonding type rmsd hydrogen bonds : bond 0.05982 ( 868) hydrogen bonds : angle 4.60392 ( 2532) covalent geometry : bond 0.00591 (13612) covalent geometry : angle 0.73790 (18454) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 294 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 53 GLN cc_start: 0.7547 (mm110) cc_final: 0.6995 (mm-40) REVERT: B 97 ASN cc_start: 0.8281 (t0) cc_final: 0.7792 (t0) REVERT: B 98 PHE cc_start: 0.8465 (t80) cc_final: 0.8085 (t80) REVERT: B 110 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7713 (mm-30) REVERT: B 224 ARG cc_start: 0.5449 (pmt170) cc_final: 0.4798 (ptm160) REVERT: B 318 LYS cc_start: 0.7380 (mptt) cc_final: 0.7085 (mptt) REVERT: A 81 GLN cc_start: 0.6630 (mp10) cc_final: 0.5979 (mp10) REVERT: A 82 GLN cc_start: 0.6759 (mm-40) cc_final: 0.6361 (mm110) REVERT: A 108 ARG cc_start: 0.6255 (mmt-90) cc_final: 0.5618 (mmt180) REVERT: A 138 LYS cc_start: 0.8148 (mmmt) cc_final: 0.7743 (mmmm) REVERT: A 165 MET cc_start: 0.5275 (ppp) cc_final: 0.5071 (ppp) REVERT: A 172 TRP cc_start: 0.6897 (t60) cc_final: 0.6535 (t60) REVERT: A 176 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7645 (tm-30) REVERT: C 53 GLN cc_start: 0.7546 (mm110) cc_final: 0.6997 (mm-40) REVERT: C 97 ASN cc_start: 0.8234 (t0) cc_final: 0.7728 (t0) REVERT: C 98 PHE cc_start: 0.8468 (t80) cc_final: 0.8092 (t80) REVERT: C 110 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7728 (mm-30) REVERT: C 224 ARG cc_start: 0.5437 (pmt170) cc_final: 0.4799 (ptm160) REVERT: C 318 LYS cc_start: 0.7389 (mptt) cc_final: 0.7089 (mptt) REVERT: D 81 GLN cc_start: 0.6587 (mp10) cc_final: 0.6028 (mp10) REVERT: D 108 ARG cc_start: 0.6278 (mmt-90) cc_final: 0.5630 (mmt180) REVERT: D 138 LYS cc_start: 0.8158 (mmmt) cc_final: 0.7752 (mmmm) REVERT: D 172 TRP cc_start: 0.6901 (t60) cc_final: 0.6544 (t60) REVERT: D 176 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7659 (tm-30) outliers start: 30 outliers final: 15 residues processed: 310 average time/residue: 0.2520 time to fit residues: 113.3649 Evaluate side-chains 245 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 230 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 318 LYS Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 46 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 117 optimal weight: 4.9990 chunk 115 optimal weight: 0.4980 chunk 82 optimal weight: 7.9990 chunk 7 optimal weight: 0.0170 chunk 2 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 144 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 408 ASN A 414 HIS C 408 ASN D 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.145437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.099405 restraints weight = 27114.514| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.56 r_work: 0.3172 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13612 Z= 0.143 Angle : 0.636 9.536 18454 Z= 0.333 Chirality : 0.044 0.177 2116 Planarity : 0.005 0.052 2306 Dihedral : 4.141 17.663 1852 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 1.40 % Allowed : 15.85 % Favored : 82.75 % 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: 0.05 (0.20), residues: 1632 helix: 0.94 (0.15), residues: 1148 sheet: None (None), residues: 0 loop : -2.19 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 172 HIS 0.004 0.001 HIS B 105 PHE 0.020 0.002 PHE A 194 TYR 0.015 0.001 TYR B 188 ARG 0.006 0.000 ARG D 61 Details of bonding type rmsd hydrogen bonds : bond 0.05028 ( 868) hydrogen bonds : angle 4.29589 ( 2532) covalent geometry : bond 0.00304 (13612) covalent geometry : angle 0.63556 (18454) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 265 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 53 GLN cc_start: 0.7584 (mm110) cc_final: 0.7018 (mm-40) REVERT: B 97 ASN cc_start: 0.8129 (t0) cc_final: 0.7579 (t0) REVERT: B 98 PHE cc_start: 0.8408 (t80) cc_final: 0.7840 (t80) REVERT: B 110 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7695 (mm-30) REVERT: B 183 MET cc_start: 0.5552 (tpt) cc_final: 0.5348 (tpt) REVERT: B 224 ARG cc_start: 0.5300 (pmt170) cc_final: 0.4535 (ptm160) REVERT: B 318 LYS cc_start: 0.7344 (mptt) cc_final: 0.7046 (mptt) REVERT: B 392 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8205 (mt) REVERT: B 418 ARG cc_start: 0.6813 (ptm-80) cc_final: 0.6301 (ttp80) REVERT: A 81 GLN cc_start: 0.6626 (mp10) cc_final: 0.5993 (mp10) REVERT: A 82 GLN cc_start: 0.6729 (mm-40) cc_final: 0.6316 (mm110) REVERT: A 92 PHE cc_start: 0.8864 (t80) cc_final: 0.8660 (t80) REVERT: A 149 GLN cc_start: 0.6498 (pp30) cc_final: 0.6226 (pp30) REVERT: A 172 TRP cc_start: 0.6841 (t60) cc_final: 0.6430 (t60) REVERT: A 176 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7600 (tm-30) REVERT: A 312 ILE cc_start: 0.8591 (mt) cc_final: 0.8389 (mt) REVERT: J 41 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8468 (tt) REVERT: C 53 GLN cc_start: 0.7572 (mm110) cc_final: 0.7006 (mm-40) REVERT: C 97 ASN cc_start: 0.8127 (t0) cc_final: 0.7581 (t0) REVERT: C 98 PHE cc_start: 0.8375 (t80) cc_final: 0.7798 (t80) REVERT: C 110 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7698 (mm-30) REVERT: C 183 MET cc_start: 0.5550 (tpt) cc_final: 0.5338 (tpt) REVERT: C 224 ARG cc_start: 0.5260 (pmt170) cc_final: 0.4512 (ptm160) REVERT: C 318 LYS cc_start: 0.7353 (mptt) cc_final: 0.7055 (mptt) REVERT: C 418 ARG cc_start: 0.6814 (ptm-80) cc_final: 0.6297 (ttp80) REVERT: D 81 GLN cc_start: 0.6607 (mp10) cc_final: 0.6072 (mp10) REVERT: D 82 GLN cc_start: 0.6627 (mm-40) cc_final: 0.6410 (mm110) REVERT: D 92 PHE cc_start: 0.8873 (t80) cc_final: 0.8671 (t80) REVERT: D 149 GLN cc_start: 0.6505 (pp30) cc_final: 0.6235 (pp30) REVERT: D 172 TRP cc_start: 0.6854 (t60) cc_final: 0.6443 (t60) REVERT: D 176 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7607 (tm-30) REVERT: E 41 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8463 (tt) outliers start: 20 outliers final: 11 residues processed: 278 average time/residue: 0.2609 time to fit residues: 107.0619 Evaluate side-chains 248 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 234 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain J residue 41 ILE Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain F residue 42 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 112 optimal weight: 0.8980 chunk 154 optimal weight: 3.9990 chunk 126 optimal weight: 0.2980 chunk 57 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 9.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 408 ASN A 414 HIS C 408 ASN D 414 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.144155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.097822 restraints weight = 26645.489| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.78 r_work: 0.3117 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13612 Z= 0.173 Angle : 0.634 8.375 18454 Z= 0.333 Chirality : 0.044 0.184 2116 Planarity : 0.005 0.052 2306 Dihedral : 4.080 18.291 1852 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.79 % Allowed : 16.90 % Favored : 80.31 % 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: 0.06 (0.21), residues: 1632 helix: 0.94 (0.15), residues: 1154 sheet: None (None), residues: 0 loop : -2.19 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 172 HIS 0.005 0.001 HIS B 306 PHE 0.022 0.002 PHE A 194 TYR 0.018 0.002 TYR C 188 ARG 0.005 0.001 ARG D 108 Details of bonding type rmsd hydrogen bonds : bond 0.05182 ( 868) hydrogen bonds : angle 4.28174 ( 2532) covalent geometry : bond 0.00393 (13612) covalent geometry : angle 0.63417 (18454) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 245 time to evaluate : 1.203 Fit side-chains REVERT: B 53 GLN cc_start: 0.7475 (mm110) cc_final: 0.6953 (mm-40) REVERT: B 97 ASN cc_start: 0.8027 (t0) cc_final: 0.7597 (t0) REVERT: B 98 PHE cc_start: 0.8462 (t80) cc_final: 0.7907 (t80) REVERT: B 224 ARG cc_start: 0.5495 (pmt170) cc_final: 0.4636 (ptm160) REVERT: B 318 LYS cc_start: 0.7232 (mptt) cc_final: 0.6996 (mptt) REVERT: B 418 ARG cc_start: 0.6886 (ptm-80) cc_final: 0.6334 (ttp80) REVERT: B 421 LYS cc_start: 0.8625 (tmmt) cc_final: 0.8331 (ptmt) REVERT: A 40 ASP cc_start: 0.2852 (m-30) cc_final: 0.2639 (m-30) REVERT: A 81 GLN cc_start: 0.6715 (mp10) cc_final: 0.6080 (mp10) REVERT: A 82 GLN cc_start: 0.6733 (mm-40) cc_final: 0.6305 (mm110) REVERT: A 92 PHE cc_start: 0.8949 (t80) cc_final: 0.8717 (t80) REVERT: A 149 GLN cc_start: 0.6454 (pp30) cc_final: 0.6206 (pm20) REVERT: A 172 TRP cc_start: 0.6735 (t60) cc_final: 0.6329 (t60) REVERT: A 176 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7642 (tm-30) REVERT: J 41 ILE cc_start: 0.8707 (mt) cc_final: 0.8455 (tt) REVERT: C 53 GLN cc_start: 0.7469 (mm110) cc_final: 0.6941 (mm-40) REVERT: C 97 ASN cc_start: 0.8034 (t0) cc_final: 0.7600 (t0) REVERT: C 98 PHE cc_start: 0.8496 (t80) cc_final: 0.7959 (t80) REVERT: C 224 ARG cc_start: 0.5454 (pmt170) cc_final: 0.4585 (ptm160) REVERT: C 271 LEU cc_start: 0.9079 (mt) cc_final: 0.8878 (mt) REVERT: C 318 LYS cc_start: 0.7215 (mptt) cc_final: 0.6975 (mptt) REVERT: C 418 ARG cc_start: 0.6890 (ptm-80) cc_final: 0.6334 (ttp80) REVERT: C 421 LYS cc_start: 0.8622 (tmmt) cc_final: 0.8328 (ptmt) REVERT: D 40 ASP cc_start: 0.2850 (m-30) cc_final: 0.2637 (m-30) REVERT: D 81 GLN cc_start: 0.6814 (mp10) cc_final: 0.6281 (mp10) REVERT: D 82 GLN cc_start: 0.6857 (mm-40) cc_final: 0.6571 (mm110) REVERT: D 149 GLN cc_start: 0.6452 (pp30) cc_final: 0.6206 (pm20) REVERT: D 172 TRP cc_start: 0.6734 (t60) cc_final: 0.6334 (t60) REVERT: D 176 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7639 (tm-30) REVERT: E 41 ILE cc_start: 0.8696 (mt) cc_final: 0.8459 (tt) outliers start: 40 outliers final: 25 residues processed: 275 average time/residue: 0.2846 time to fit residues: 116.1229 Evaluate side-chains 247 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 222 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 318 LYS Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain F residue 42 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 46 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 44 optimal weight: 0.0570 chunk 148 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 134 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 ASN A 414 HIS D 414 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.145936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.100709 restraints weight = 27021.351| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.76 r_work: 0.3177 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13612 Z= 0.133 Angle : 0.607 8.265 18454 Z= 0.318 Chirality : 0.043 0.190 2116 Planarity : 0.004 0.053 2306 Dihedral : 3.979 17.669 1852 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.86 % Allowed : 18.85 % Favored : 78.28 % 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: 0.17 (0.21), residues: 1632 helix: 1.03 (0.15), residues: 1154 sheet: None (None), residues: 0 loop : -2.16 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 172 HIS 0.004 0.001 HIS B 94 PHE 0.021 0.002 PHE C 343 TYR 0.015 0.001 TYR C 188 ARG 0.004 0.000 ARG A 108 Details of bonding type rmsd hydrogen bonds : bond 0.04679 ( 868) hydrogen bonds : angle 4.15376 ( 2532) covalent geometry : bond 0.00286 (13612) covalent geometry : angle 0.60713 (18454) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 252 time to evaluate : 1.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 53 GLN cc_start: 0.7565 (mm110) cc_final: 0.6989 (mm-40) REVERT: B 97 ASN cc_start: 0.7860 (t0) cc_final: 0.7573 (t0) REVERT: B 98 PHE cc_start: 0.8443 (t80) cc_final: 0.7891 (t80) REVERT: B 175 PHE cc_start: 0.7286 (OUTLIER) cc_final: 0.6362 (t80) REVERT: B 224 ARG cc_start: 0.5416 (pmt170) cc_final: 0.4447 (ptm160) REVERT: B 318 LYS cc_start: 0.7337 (mptt) cc_final: 0.7096 (mptt) REVERT: B 392 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8257 (mt) REVERT: B 418 ARG cc_start: 0.6714 (ptm-80) cc_final: 0.6242 (ttp80) REVERT: B 421 LYS cc_start: 0.8458 (tmmt) cc_final: 0.8203 (ptmt) REVERT: A 40 ASP cc_start: 0.2824 (m-30) cc_final: 0.2528 (m-30) REVERT: A 81 GLN cc_start: 0.6714 (mp10) cc_final: 0.6082 (mp10) REVERT: A 82 GLN cc_start: 0.6791 (mm-40) cc_final: 0.6383 (mm110) REVERT: A 149 GLN cc_start: 0.6469 (pp30) cc_final: 0.6048 (pp30) REVERT: A 176 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7617 (tm-30) REVERT: J 41 ILE cc_start: 0.8667 (mt) cc_final: 0.8434 (tt) REVERT: C 53 GLN cc_start: 0.7517 (mm110) cc_final: 0.6936 (mm-40) REVERT: C 97 ASN cc_start: 0.7857 (t0) cc_final: 0.7564 (t0) REVERT: C 98 PHE cc_start: 0.8427 (t80) cc_final: 0.7875 (t80) REVERT: C 175 PHE cc_start: 0.7284 (OUTLIER) cc_final: 0.6357 (t80) REVERT: C 224 ARG cc_start: 0.5398 (pmt170) cc_final: 0.4423 (ptm160) REVERT: C 318 LYS cc_start: 0.7329 (mptt) cc_final: 0.7086 (mptt) REVERT: C 392 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8268 (mt) REVERT: C 418 ARG cc_start: 0.6718 (ptm-80) cc_final: 0.6248 (ttp80) REVERT: C 421 LYS cc_start: 0.8478 (tmmt) cc_final: 0.8222 (ptmt) REVERT: D 40 ASP cc_start: 0.2835 (m-30) cc_final: 0.2549 (m-30) REVERT: D 81 GLN cc_start: 0.6747 (mp10) cc_final: 0.6244 (mp10) REVERT: D 82 GLN cc_start: 0.6827 (mm-40) cc_final: 0.6482 (mm110) REVERT: D 90 ASP cc_start: 0.8636 (m-30) cc_final: 0.8412 (m-30) REVERT: D 149 GLN cc_start: 0.6480 (pp30) cc_final: 0.6055 (pp30) REVERT: D 176 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7618 (tm-30) REVERT: E 41 ILE cc_start: 0.8663 (mt) cc_final: 0.8441 (tt) outliers start: 41 outliers final: 21 residues processed: 287 average time/residue: 0.2468 time to fit residues: 105.1897 Evaluate side-chains 255 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 230 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 188 TYR Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 188 TYR Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain F residue 42 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 107 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 145 optimal weight: 4.9990 chunk 118 optimal weight: 0.4980 chunk 117 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 chunk 88 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN A 414 HIS C 46 ASN D 202 ASN D 414 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.145322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.100752 restraints weight = 27014.255| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.64 r_work: 0.3161 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13612 Z= 0.155 Angle : 0.636 8.693 18454 Z= 0.333 Chirality : 0.044 0.254 2116 Planarity : 0.005 0.055 2306 Dihedral : 3.968 18.097 1852 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.63 % Allowed : 19.69 % Favored : 76.68 % 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: 0.23 (0.21), residues: 1632 helix: 1.08 (0.15), residues: 1154 sheet: None (None), residues: 0 loop : -2.16 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 172 HIS 0.004 0.001 HIS D 306 PHE 0.021 0.002 PHE B 343 TYR 0.017 0.002 TYR B 188 ARG 0.004 0.000 ARG A 108 Details of bonding type rmsd hydrogen bonds : bond 0.04889 ( 868) hydrogen bonds : angle 4.18184 ( 2532) covalent geometry : bond 0.00346 (13612) covalent geometry : angle 0.63571 (18454) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 249 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 53 GLN cc_start: 0.7404 (mm110) cc_final: 0.6836 (mm-40) REVERT: B 97 ASN cc_start: 0.7902 (t0) cc_final: 0.7676 (t0) REVERT: B 98 PHE cc_start: 0.8437 (t80) cc_final: 0.7868 (t80) REVERT: B 175 PHE cc_start: 0.7300 (OUTLIER) cc_final: 0.6346 (t80) REVERT: B 224 ARG cc_start: 0.5631 (pmt170) cc_final: 0.4690 (ptm160) REVERT: B 318 LYS cc_start: 0.7390 (mptt) cc_final: 0.7153 (mptt) REVERT: B 392 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8247 (mt) REVERT: B 418 ARG cc_start: 0.6606 (ptm-80) cc_final: 0.6104 (ttp80) REVERT: B 421 LYS cc_start: 0.8467 (tmmt) cc_final: 0.8149 (ptmt) REVERT: A 81 GLN cc_start: 0.6700 (mp10) cc_final: 0.6054 (mp10) REVERT: A 82 GLN cc_start: 0.6816 (mm-40) cc_final: 0.6390 (mm110) REVERT: A 90 ASP cc_start: 0.8542 (m-30) cc_final: 0.8333 (m-30) REVERT: A 149 GLN cc_start: 0.6483 (pp30) cc_final: 0.6256 (pm20) REVERT: A 176 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7620 (tm-30) REVERT: J 41 ILE cc_start: 0.8679 (mt) cc_final: 0.8444 (tt) REVERT: C 53 GLN cc_start: 0.7403 (mm110) cc_final: 0.6825 (mm-40) REVERT: C 97 ASN cc_start: 0.7898 (t0) cc_final: 0.7662 (t0) REVERT: C 98 PHE cc_start: 0.8432 (t80) cc_final: 0.7865 (t80) REVERT: C 175 PHE cc_start: 0.7311 (OUTLIER) cc_final: 0.6359 (t80) REVERT: C 224 ARG cc_start: 0.5610 (pmt170) cc_final: 0.4666 (ptm160) REVERT: C 318 LYS cc_start: 0.7386 (mptt) cc_final: 0.7147 (mptt) REVERT: C 392 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8336 (mt) REVERT: C 418 ARG cc_start: 0.6612 (ptm-80) cc_final: 0.6105 (ttp80) REVERT: C 421 LYS cc_start: 0.8469 (tmmt) cc_final: 0.8151 (ptmt) REVERT: D 81 GLN cc_start: 0.6652 (mp10) cc_final: 0.6154 (mp10) REVERT: D 82 GLN cc_start: 0.6933 (mm-40) cc_final: 0.6605 (mm110) REVERT: D 90 ASP cc_start: 0.8646 (m-30) cc_final: 0.8430 (m-30) REVERT: D 149 GLN cc_start: 0.6484 (pp30) cc_final: 0.6262 (pm20) REVERT: D 176 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7625 (tm-30) REVERT: E 41 ILE cc_start: 0.8677 (mt) cc_final: 0.8448 (tt) outliers start: 52 outliers final: 32 residues processed: 284 average time/residue: 0.2428 time to fit residues: 101.5428 Evaluate side-chains 265 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 229 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 188 TYR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 188 TYR Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 318 LYS Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain F residue 42 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 25 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 130 optimal weight: 7.9990 chunk 151 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 HIS D 414 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.145555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.101868 restraints weight = 26904.596| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.63 r_work: 0.3167 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13612 Z= 0.150 Angle : 0.629 10.451 18454 Z= 0.327 Chirality : 0.043 0.230 2116 Planarity : 0.004 0.052 2306 Dihedral : 3.965 18.125 1852 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.91 % Allowed : 19.97 % Favored : 76.12 % 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: 0.28 (0.21), residues: 1632 helix: 1.12 (0.15), residues: 1154 sheet: None (None), residues: 0 loop : -2.15 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 172 HIS 0.004 0.001 HIS A 306 PHE 0.020 0.002 PHE B 343 TYR 0.017 0.001 TYR B 188 ARG 0.004 0.000 ARG D 147 Details of bonding type rmsd hydrogen bonds : bond 0.04749 ( 868) hydrogen bonds : angle 4.16717 ( 2532) covalent geometry : bond 0.00335 (13612) covalent geometry : angle 0.62877 (18454) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 246 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 53 GLN cc_start: 0.7371 (mm110) cc_final: 0.6770 (mm-40) REVERT: B 98 PHE cc_start: 0.8444 (t80) cc_final: 0.8188 (t80) REVERT: B 138 LYS cc_start: 0.8380 (mmmt) cc_final: 0.8172 (mmtm) REVERT: B 175 PHE cc_start: 0.7297 (OUTLIER) cc_final: 0.6339 (t80) REVERT: B 224 ARG cc_start: 0.5562 (pmt170) cc_final: 0.4664 (ptm160) REVERT: B 248 LEU cc_start: 0.7302 (tt) cc_final: 0.7055 (tp) REVERT: B 318 LYS cc_start: 0.7408 (mptt) cc_final: 0.7169 (mptt) REVERT: B 392 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8254 (mt) REVERT: B 418 ARG cc_start: 0.6625 (ptm-80) cc_final: 0.6105 (ttp80) REVERT: B 421 LYS cc_start: 0.8471 (tmmt) cc_final: 0.8136 (ptmt) REVERT: A 81 GLN cc_start: 0.6781 (mp10) cc_final: 0.6280 (mp10) REVERT: A 108 ARG cc_start: 0.6538 (mmt-90) cc_final: 0.5956 (mmt180) REVERT: A 176 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7613 (tm-30) REVERT: J 41 ILE cc_start: 0.8654 (mt) cc_final: 0.8423 (tt) REVERT: C 53 GLN cc_start: 0.7363 (mm110) cc_final: 0.6760 (mm-40) REVERT: C 98 PHE cc_start: 0.8439 (t80) cc_final: 0.8184 (t80) REVERT: C 138 LYS cc_start: 0.8389 (mmmt) cc_final: 0.8120 (mmtm) REVERT: C 175 PHE cc_start: 0.7305 (OUTLIER) cc_final: 0.6351 (t80) REVERT: C 224 ARG cc_start: 0.5547 (pmt170) cc_final: 0.4648 (ptm160) REVERT: C 248 LEU cc_start: 0.7307 (tt) cc_final: 0.7059 (tp) REVERT: C 318 LYS cc_start: 0.7411 (mptt) cc_final: 0.7167 (mptt) REVERT: C 392 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8344 (mt) REVERT: C 418 ARG cc_start: 0.6619 (ptm-80) cc_final: 0.6103 (ttp80) REVERT: C 421 LYS cc_start: 0.8477 (tmmt) cc_final: 0.8140 (ptmt) REVERT: D 81 GLN cc_start: 0.6662 (mp10) cc_final: 0.6161 (mp10) REVERT: D 82 GLN cc_start: 0.6955 (mm-40) cc_final: 0.6638 (mm110) REVERT: D 108 ARG cc_start: 0.6543 (mmt-90) cc_final: 0.5960 (mmt180) REVERT: D 149 GLN cc_start: 0.6530 (pp30) cc_final: 0.6330 (pm20) REVERT: D 176 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7614 (tm-30) REVERT: E 41 ILE cc_start: 0.8678 (mt) cc_final: 0.8452 (tt) outliers start: 56 outliers final: 42 residues processed: 287 average time/residue: 0.2620 time to fit residues: 108.7278 Evaluate side-chains 280 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 234 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 188 TYR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 188 TYR Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 318 LYS Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 42 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 5 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 414 HIS D 414 HIS 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 = 0.145271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.097088 restraints weight = 26939.178| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.51 r_work: 0.3169 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13612 Z= 0.163 Angle : 0.653 15.317 18454 Z= 0.339 Chirality : 0.045 0.462 2116 Planarity : 0.005 0.052 2306 Dihedral : 3.984 18.483 1852 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.98 % Allowed : 20.18 % Favored : 75.84 % 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: 0.26 (0.21), residues: 1632 helix: 1.10 (0.15), residues: 1146 sheet: None (None), residues: 0 loop : -2.09 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 172 HIS 0.004 0.001 HIS C 94 PHE 0.020 0.002 PHE B 343 TYR 0.018 0.002 TYR C 188 ARG 0.004 0.000 ARG A 147 Details of bonding type rmsd hydrogen bonds : bond 0.04910 ( 868) hydrogen bonds : angle 4.20264 ( 2532) covalent geometry : bond 0.00373 (13612) covalent geometry : angle 0.65271 (18454) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 246 time to evaluate : 1.521 Fit side-chains REVERT: B 53 GLN cc_start: 0.7336 (mm110) cc_final: 0.6752 (mm-40) REVERT: B 98 PHE cc_start: 0.8258 (t80) cc_final: 0.7922 (t80) REVERT: B 118 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7526 (tp30) REVERT: B 138 LYS cc_start: 0.8414 (mmmt) cc_final: 0.8094 (mmtm) REVERT: B 175 PHE cc_start: 0.7284 (OUTLIER) cc_final: 0.6314 (t80) REVERT: B 219 LEU cc_start: 0.4720 (OUTLIER) cc_final: 0.4495 (pp) REVERT: B 224 ARG cc_start: 0.5707 (pmt170) cc_final: 0.4708 (ptm160) REVERT: B 248 LEU cc_start: 0.7311 (tt) cc_final: 0.7071 (tp) REVERT: B 318 LYS cc_start: 0.7392 (mptt) cc_final: 0.7146 (mptt) REVERT: B 392 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8291 (mt) REVERT: B 418 ARG cc_start: 0.6636 (ptm-80) cc_final: 0.6161 (ttp80) REVERT: A 81 GLN cc_start: 0.6779 (mp10) cc_final: 0.6293 (mp10) REVERT: A 108 ARG cc_start: 0.6598 (mmt-90) cc_final: 0.5967 (mmt180) REVERT: A 149 GLN cc_start: 0.6315 (pm20) cc_final: 0.6045 (pm20) REVERT: A 176 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7584 (tm-30) REVERT: A 187 PHE cc_start: 0.7286 (t80) cc_final: 0.7018 (t80) REVERT: A 312 ILE cc_start: 0.8618 (mt) cc_final: 0.8400 (mt) REVERT: J 41 ILE cc_start: 0.8655 (mt) cc_final: 0.8422 (tt) REVERT: C 53 GLN cc_start: 0.7345 (mm110) cc_final: 0.6753 (mm-40) REVERT: C 98 PHE cc_start: 0.8254 (t80) cc_final: 0.7914 (t80) REVERT: C 118 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7568 (tp30) REVERT: C 138 LYS cc_start: 0.8418 (mmmt) cc_final: 0.8097 (mmtm) REVERT: C 175 PHE cc_start: 0.7284 (OUTLIER) cc_final: 0.6309 (t80) REVERT: C 219 LEU cc_start: 0.4669 (OUTLIER) cc_final: 0.4435 (pp) REVERT: C 224 ARG cc_start: 0.5699 (pmt170) cc_final: 0.4692 (ptm160) REVERT: C 248 LEU cc_start: 0.7329 (tt) cc_final: 0.7090 (tp) REVERT: C 318 LYS cc_start: 0.7389 (mptt) cc_final: 0.7139 (mptt) REVERT: C 392 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8370 (mt) REVERT: C 418 ARG cc_start: 0.6648 (ptm-80) cc_final: 0.6171 (ttp80) REVERT: D 81 GLN cc_start: 0.6721 (mp10) cc_final: 0.6144 (mp10) REVERT: D 82 GLN cc_start: 0.6957 (mm-40) cc_final: 0.6641 (mm110) REVERT: D 108 ARG cc_start: 0.6587 (mmt-90) cc_final: 0.5978 (mmt180) REVERT: D 176 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7590 (tm-30) REVERT: D 187 PHE cc_start: 0.7272 (t80) cc_final: 0.7003 (t80) REVERT: E 41 ILE cc_start: 0.8675 (mt) cc_final: 0.8446 (tt) outliers start: 57 outliers final: 45 residues processed: 288 average time/residue: 0.2706 time to fit residues: 111.6975 Evaluate side-chains 285 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 234 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 188 TYR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 188 TYR Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 318 LYS Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 42 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 72 optimal weight: 0.5980 chunk 20 optimal weight: 9.9990 chunk 131 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 414 HIS D 414 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.146578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.100898 restraints weight = 26667.293| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.73 r_work: 0.3147 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13612 Z= 0.141 Angle : 0.639 12.930 18454 Z= 0.329 Chirality : 0.044 0.381 2116 Planarity : 0.004 0.053 2306 Dihedral : 3.959 18.140 1852 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.70 % Allowed : 20.88 % Favored : 75.42 % 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: 0.34 (0.21), residues: 1632 helix: 1.14 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -1.97 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 172 HIS 0.004 0.001 HIS A 306 PHE 0.019 0.001 PHE C 343 TYR 0.017 0.001 TYR B 188 ARG 0.006 0.000 ARG D 147 Details of bonding type rmsd hydrogen bonds : bond 0.04595 ( 868) hydrogen bonds : angle 4.12854 ( 2532) covalent geometry : bond 0.00311 (13612) covalent geometry : angle 0.63902 (18454) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 255 time to evaluate : 1.510 Fit side-chains REVERT: B 53 GLN cc_start: 0.7333 (mm110) cc_final: 0.6739 (mm-40) REVERT: B 98 PHE cc_start: 0.8253 (t80) cc_final: 0.7924 (t80) REVERT: B 118 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7550 (tp30) REVERT: B 138 LYS cc_start: 0.8380 (mmmt) cc_final: 0.8146 (mmtm) REVERT: B 175 PHE cc_start: 0.7267 (OUTLIER) cc_final: 0.6325 (t80) REVERT: B 219 LEU cc_start: 0.4595 (OUTLIER) cc_final: 0.4367 (pp) REVERT: B 224 ARG cc_start: 0.5771 (pmt170) cc_final: 0.4697 (ptm160) REVERT: B 248 LEU cc_start: 0.7342 (tt) cc_final: 0.7118 (tp) REVERT: B 318 LYS cc_start: 0.7402 (mptt) cc_final: 0.7154 (mptt) REVERT: B 392 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8200 (mt) REVERT: B 418 ARG cc_start: 0.6670 (ptm-80) cc_final: 0.6067 (ttp80) REVERT: B 421 LYS cc_start: 0.8458 (tmmt) cc_final: 0.8152 (ptmt) REVERT: A 81 GLN cc_start: 0.6750 (mp10) cc_final: 0.6189 (mp10) REVERT: A 108 ARG cc_start: 0.6633 (mmt-90) cc_final: 0.5943 (mmt180) REVERT: A 132 CYS cc_start: 0.3939 (p) cc_final: 0.2605 (t) REVERT: A 149 GLN cc_start: 0.6329 (pm20) cc_final: 0.6053 (pm20) REVERT: A 172 TRP cc_start: 0.6459 (t60) cc_final: 0.6182 (t60) REVERT: A 176 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7581 (tm-30) REVERT: J 41 ILE cc_start: 0.8641 (mt) cc_final: 0.8404 (tt) REVERT: C 53 GLN cc_start: 0.7344 (mm110) cc_final: 0.6745 (mm-40) REVERT: C 98 PHE cc_start: 0.8251 (t80) cc_final: 0.7920 (t80) REVERT: C 118 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7580 (tp30) REVERT: C 138 LYS cc_start: 0.8397 (mmmt) cc_final: 0.8101 (mmtm) REVERT: C 175 PHE cc_start: 0.7252 (OUTLIER) cc_final: 0.6311 (t80) REVERT: C 219 LEU cc_start: 0.4603 (OUTLIER) cc_final: 0.4370 (pp) REVERT: C 224 ARG cc_start: 0.5750 (pmt170) cc_final: 0.4685 (ptm160) REVERT: C 248 LEU cc_start: 0.7346 (tt) cc_final: 0.7079 (tp) REVERT: C 318 LYS cc_start: 0.7391 (mptt) cc_final: 0.7137 (mptt) REVERT: C 392 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8288 (mt) REVERT: C 418 ARG cc_start: 0.6683 (ptm-80) cc_final: 0.6075 (ttp80) REVERT: C 421 LYS cc_start: 0.8466 (tmmt) cc_final: 0.8160 (ptmt) REVERT: D 81 GLN cc_start: 0.6710 (mp10) cc_final: 0.6132 (mp10) REVERT: D 82 GLN cc_start: 0.7049 (mm-40) cc_final: 0.6749 (mm110) REVERT: D 108 ARG cc_start: 0.6636 (mmt-90) cc_final: 0.6017 (mmt180) REVERT: D 149 GLN cc_start: 0.6427 (pm20) cc_final: 0.6186 (pm20) REVERT: D 172 TRP cc_start: 0.6457 (t60) cc_final: 0.6181 (t60) REVERT: D 176 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7585 (tm-30) REVERT: E 41 ILE cc_start: 0.8661 (mt) cc_final: 0.8429 (tt) outliers start: 53 outliers final: 38 residues processed: 294 average time/residue: 0.2945 time to fit residues: 124.1366 Evaluate side-chains 284 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 240 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 188 TYR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain J residue 46 SER Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 188 TYR Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 318 LYS Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 42 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 137 optimal weight: 0.8980 chunk 145 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 105 optimal weight: 0.0670 chunk 135 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 142 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 414 HIS D 414 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.146819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.100626 restraints weight = 26753.421| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.68 r_work: 0.3177 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13612 Z= 0.142 Angle : 0.651 11.991 18454 Z= 0.337 Chirality : 0.045 0.345 2116 Planarity : 0.005 0.051 2306 Dihedral : 3.946 17.329 1852 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.07 % Allowed : 21.72 % Favored : 75.21 % 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: 0.33 (0.21), residues: 1632 helix: 1.12 (0.15), residues: 1142 sheet: None (None), residues: 0 loop : -1.97 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 172 HIS 0.004 0.001 HIS D 306 PHE 0.021 0.002 PHE A 187 TYR 0.020 0.001 TYR A 76 ARG 0.004 0.000 ARG A 147 Details of bonding type rmsd hydrogen bonds : bond 0.04661 ( 868) hydrogen bonds : angle 4.13915 ( 2532) covalent geometry : bond 0.00315 (13612) covalent geometry : angle 0.65132 (18454) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3264 Ramachandran restraints generated. 1632 Oldfield, 0 Emsley, 1632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 239 time to evaluate : 1.384 Fit side-chains REVERT: B 53 GLN cc_start: 0.7333 (mm110) cc_final: 0.6727 (mm-40) REVERT: B 98 PHE cc_start: 0.8324 (t80) cc_final: 0.8021 (t80) REVERT: B 118 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7523 (tp30) REVERT: B 138 LYS cc_start: 0.8359 (mmmt) cc_final: 0.8127 (mmtm) REVERT: B 175 PHE cc_start: 0.7246 (OUTLIER) cc_final: 0.6335 (t80) REVERT: B 219 LEU cc_start: 0.4625 (OUTLIER) cc_final: 0.4398 (pp) REVERT: B 224 ARG cc_start: 0.5761 (pmt170) cc_final: 0.4711 (ptm160) REVERT: B 248 LEU cc_start: 0.7360 (tt) cc_final: 0.7111 (tp) REVERT: B 318 LYS cc_start: 0.7382 (mptt) cc_final: 0.7129 (mptt) REVERT: B 392 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8179 (mt) REVERT: B 418 ARG cc_start: 0.6679 (ptm-80) cc_final: 0.6121 (ttp80) REVERT: A 81 GLN cc_start: 0.6685 (mp10) cc_final: 0.6154 (mp10) REVERT: A 108 ARG cc_start: 0.6597 (mmt-90) cc_final: 0.5933 (mmt180) REVERT: A 132 CYS cc_start: 0.3995 (p) cc_final: 0.2887 (t) REVERT: A 149 GLN cc_start: 0.6394 (OUTLIER) cc_final: 0.6108 (pm20) REVERT: A 172 TRP cc_start: 0.6440 (t60) cc_final: 0.6200 (t60) REVERT: A 176 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7575 (tm-30) REVERT: J 41 ILE cc_start: 0.8632 (mt) cc_final: 0.8406 (tt) REVERT: C 53 GLN cc_start: 0.7338 (mm110) cc_final: 0.6729 (mm-40) REVERT: C 98 PHE cc_start: 0.8251 (t80) cc_final: 0.7929 (t80) REVERT: C 118 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7566 (tp30) REVERT: C 138 LYS cc_start: 0.8365 (mmmt) cc_final: 0.8133 (mmtm) REVERT: C 175 PHE cc_start: 0.7225 (OUTLIER) cc_final: 0.6298 (t80) REVERT: C 219 LEU cc_start: 0.4637 (OUTLIER) cc_final: 0.4401 (pp) REVERT: C 224 ARG cc_start: 0.5748 (pmt170) cc_final: 0.4689 (ptm160) REVERT: C 248 LEU cc_start: 0.7460 (tt) cc_final: 0.7185 (tp) REVERT: C 318 LYS cc_start: 0.7356 (mptt) cc_final: 0.7102 (mptt) REVERT: C 392 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8273 (mt) REVERT: C 418 ARG cc_start: 0.6676 (ptm-80) cc_final: 0.6122 (ttp80) REVERT: D 81 GLN cc_start: 0.6608 (mp10) cc_final: 0.6063 (mp10) REVERT: D 82 GLN cc_start: 0.7050 (mm-40) cc_final: 0.6772 (mm110) REVERT: D 108 ARG cc_start: 0.6580 (mmt-90) cc_final: 0.5904 (mmt180) REVERT: D 132 CYS cc_start: 0.4000 (p) cc_final: 0.2877 (t) REVERT: D 149 GLN cc_start: 0.6416 (pm20) cc_final: 0.6171 (pm20) REVERT: D 172 TRP cc_start: 0.6439 (t60) cc_final: 0.6195 (t60) REVERT: D 176 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7580 (tm-30) REVERT: E 41 ILE cc_start: 0.8629 (mt) cc_final: 0.8399 (tt) outliers start: 44 outliers final: 33 residues processed: 275 average time/residue: 0.2281 time to fit residues: 92.6785 Evaluate side-chains 270 residues out of total 1432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 230 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 188 TYR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 231 CYS Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 188 TYR Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 236 CYS Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 53 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 29 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 50 optimal weight: 7.9990 chunk 62 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 144 optimal weight: 7.9990 chunk 112 optimal weight: 0.6980 chunk 17 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 414 HIS D 414 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.146002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.098740 restraints weight = 26916.955| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.80 r_work: 0.3161 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13612 Z= 0.161 Angle : 0.679 16.121 18454 Z= 0.344 Chirality : 0.045 0.494 2116 Planarity : 0.005 0.050 2306 Dihedral : 3.996 17.622 1852 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.42 % Allowed : 21.02 % Favored : 75.56 % 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: 0.25 (0.21), residues: 1632 helix: 1.07 (0.15), residues: 1142 sheet: None (None), residues: 0 loop : -2.01 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 172 HIS 0.004 0.001 HIS D 306 PHE 0.019 0.002 PHE C 343 TYR 0.018 0.001 TYR B 188 ARG 0.004 0.000 ARG A 147 Details of bonding type rmsd hydrogen bonds : bond 0.04787 ( 868) hydrogen bonds : angle 4.19186 ( 2532) covalent geometry : bond 0.00366 (13612) covalent geometry : angle 0.67883 (18454) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8128.40 seconds wall clock time: 146 minutes 37.17 seconds (8797.17 seconds total)