Starting phenix.real_space_refine on Sun May 11 14:50:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9as4_43804/05_2025/9as4_43804.cif Found real_map, /net/cci-nas-00/data/ceres_data/9as4_43804/05_2025/9as4_43804.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9as4_43804/05_2025/9as4_43804.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9as4_43804/05_2025/9as4_43804.map" model { file = "/net/cci-nas-00/data/ceres_data/9as4_43804/05_2025/9as4_43804.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9as4_43804/05_2025/9as4_43804.cif" } resolution = 3.06 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= 0.030 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 56 5.16 5 C 5228 2.51 5 N 1376 2.21 5 O 1509 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8169 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1866 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 8, 'TRANS': 236} Chain breaks: 4 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 58 Chain: "B" Number of atoms: 1746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1746 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 4, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 6, 'PHE:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 64 Chain: "C" Number of atoms: 2482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2482 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 325} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "D" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 342 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1709 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 217} Chain breaks: 2 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'7LD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.23, per 1000 atoms: 0.64 Number of scatterers: 8169 At special positions: 0 Unit cell: (84.48, 119.68, 125.84, 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 56 16.00 O 1509 8.00 N 1376 7.00 C 5228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 227 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.05 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 936.1 milliseconds 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2016 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 15 sheets defined 35.0% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 84 through 99 removed outlier: 3.639A pdb=" N LEU A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N MET A 97 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 122 removed outlier: 3.805A pdb=" N LEU A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 137 Processing helix chain 'A' and resid 147 through 179 Processing helix chain 'A' and resid 179 through 186 removed outlier: 3.824A pdb=" N PHE A 186 " --> pdb=" O HIS A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 207 removed outlier: 3.753A pdb=" N SER A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 213 removed outlier: 3.642A pdb=" N VAL A 212 " --> pdb=" O MET A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.524A pdb=" N ILE A 237 " --> pdb=" O ASN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 261 Processing helix chain 'A' and resid 316 through 347 Proline residue: A 338 - end of helix removed outlier: 3.863A pdb=" N VAL A 347 " --> pdb=" O ASN A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 382 removed outlier: 3.775A pdb=" N TRP A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA A 374 " --> pdb=" O TYR A 370 " (cutoff:3.500A) Proline residue: A 377 - end of helix removed outlier: 3.512A pdb=" N THR A 381 " --> pdb=" O PRO A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 393 Processing helix chain 'B' and resid 6 through 33 removed outlier: 3.899A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N THR B 33 " --> pdb=" O LYS B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 115 through 130 removed outlier: 4.047A pdb=" N GLN B 119 " --> pdb=" O TYR B 115 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLU B 120 " --> pdb=" O ASN B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 156 Processing helix chain 'B' and resid 159 through 164 removed outlier: 3.794A pdb=" N TYR B 163 " --> pdb=" O LYS B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 removed outlier: 4.253A pdb=" N ALA B 168 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARG B 169 " --> pdb=" O PRO B 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 164 through 169' Processing helix chain 'B' and resid 183 through 203 removed outlier: 3.824A pdb=" N PHE B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 243 Processing helix chain 'C' and resid 11 through 26 Processing helix chain 'C' and resid 29 through 35 Processing helix chain 'D' and resid 13 through 24 removed outlier: 3.530A pdb=" N GLU D 17 " --> pdb=" O ARG D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.136A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.540A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 70 through 76 removed outlier: 6.837A pdb=" N ARG B 35 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE B 107 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU B 37 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL B 109 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU B 39 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N ASP B 111 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE B 106 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N PHE B 142 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N PHE B 108 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ASN B 144 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL B 110 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.610A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 102 through 105 removed outlier: 5.984A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.390A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 3.662A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.583A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.585A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP C 303 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.799A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 33 through 34 removed outlier: 4.438A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 49 through 51 Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.361A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 143 through 148 Processing sheet with id=AB6, first strand: chain 'E' and resid 182 through 183 removed outlier: 6.618A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) 394 hydrogen bonds defined for protein. 1101 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: 2.17 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2601 1.34 - 1.46: 1885 1.46 - 1.58: 3767 1.58 - 1.70: 1 1.70 - 1.82: 84 Bond restraints: 8338 Sorted by residual: bond pdb=" N CYS C 148 " pdb=" CA CYS C 148 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.21e-02 6.83e+03 7.45e+00 bond pdb=" N HIS B 209 " pdb=" CA HIS B 209 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.25e-02 6.40e+03 7.36e+00 bond pdb=" CA SER A 188 " pdb=" CB SER A 188 " ideal model delta sigma weight residual 1.528 1.492 0.036 1.34e-02 5.57e+03 7.31e+00 bond pdb=" N ASN A 384 " pdb=" CA ASN A 384 " ideal model delta sigma weight residual 1.456 1.490 -0.033 1.29e-02 6.01e+03 6.72e+00 bond pdb=" N ASN A 107 " pdb=" CA ASN A 107 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.31e-02 5.83e+03 6.63e+00 ... (remaining 8333 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 10851 1.96 - 3.92: 407 3.92 - 5.88: 65 5.88 - 7.84: 13 7.84 - 9.80: 2 Bond angle restraints: 11338 Sorted by residual: angle pdb=" CA LYS E 43 " pdb=" CB LYS E 43 " pdb=" CG LYS E 43 " ideal model delta sigma weight residual 114.10 123.90 -9.80 2.00e+00 2.50e-01 2.40e+01 angle pdb=" CA PRO A 377 " pdb=" N PRO A 377 " pdb=" CD PRO A 377 " ideal model delta sigma weight residual 112.00 105.79 6.21 1.40e+00 5.10e-01 1.97e+01 angle pdb=" N ASP C 170 " pdb=" CA ASP C 170 " pdb=" C ASP C 170 " ideal model delta sigma weight residual 107.99 101.16 6.83 1.77e+00 3.19e-01 1.49e+01 angle pdb=" CA ASP B 220 " pdb=" CB ASP B 220 " pdb=" CG ASP B 220 " ideal model delta sigma weight residual 112.60 116.31 -3.71 1.00e+00 1.00e+00 1.38e+01 angle pdb=" N ASP C 154 " pdb=" CA ASP C 154 " pdb=" C ASP C 154 " ideal model delta sigma weight residual 112.89 108.33 4.56 1.24e+00 6.50e-01 1.35e+01 ... (remaining 11333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.50: 4779 34.50 - 68.99: 117 68.99 - 103.49: 8 103.49 - 137.98: 0 137.98 - 172.48: 1 Dihedral angle restraints: 4905 sinusoidal: 1786 harmonic: 3119 Sorted by residual: dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual -86.00 -38.88 -47.12 1 1.00e+01 1.00e-02 3.07e+01 dihedral pdb=" CA THR C 128 " pdb=" C THR C 128 " pdb=" N ARG C 129 " pdb=" CA ARG C 129 " ideal model delta harmonic sigma weight residual 180.00 155.31 24.69 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA LYS A 223 " pdb=" C LYS A 223 " pdb=" N GLU A 224 " pdb=" CA GLU A 224 " ideal model delta harmonic sigma weight residual 180.00 155.79 24.21 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 4902 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1014 0.052 - 0.103: 236 0.103 - 0.155: 65 0.155 - 0.207: 7 0.207 - 0.259: 2 Chirality restraints: 1324 Sorted by residual: chirality pdb=" C11 7LD A 501 " pdb=" C15 7LD A 501 " pdb=" C9 7LD A 501 " pdb=" N2 7LD A 501 " both_signs ideal model delta sigma weight residual False 2.48 2.22 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA ILE C 58 " pdb=" N ILE C 58 " pdb=" C ILE C 58 " pdb=" CB ILE C 58 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA VAL B 86 " pdb=" N VAL B 86 " pdb=" C VAL B 86 " pdb=" CB VAL B 86 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.29e-01 ... (remaining 1321 not shown) Planarity restraints: 1425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 376 " 0.074 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO A 377 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO A 377 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 377 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 245 " -0.044 5.00e-02 4.00e+02 6.70e-02 7.19e+00 pdb=" N PRO A 246 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 246 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 246 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 141 " 0.040 5.00e-02 4.00e+02 6.05e-02 5.86e+00 pdb=" N PRO A 142 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 142 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 142 " 0.035 5.00e-02 4.00e+02 ... (remaining 1422 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 96 2.62 - 3.19: 6931 3.19 - 3.76: 12371 3.76 - 4.33: 17485 4.33 - 4.90: 29986 Nonbonded interactions: 66869 Sorted by model distance: nonbonded pdb=" OG1 THR B 221 " pdb=" OE1 GLU B 222 " model vdw 2.046 3.040 nonbonded pdb=" O GLY E 9 " pdb=" NH1 ARG E 18 " model vdw 2.233 3.120 nonbonded pdb=" ND2 ASN C 230 " pdb=" OD1 ASP C 246 " model vdw 2.234 3.120 nonbonded pdb=" O PRO A 377 " pdb=" OG1 THR A 381 " model vdw 2.269 3.040 nonbonded pdb=" O GLN C 75 " pdb=" OG SER C 98 " model vdw 2.278 3.040 ... (remaining 66864 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.290 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 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 : 0.005 0.061 8341 Z= 0.262 Angle : 0.885 9.800 11344 Z= 0.487 Chirality : 0.049 0.259 1324 Planarity : 0.007 0.108 1425 Dihedral : 15.788 172.476 2880 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.47 % Allowed : 18.24 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 0.36 (0.24), residues: 1052 helix: 0.12 (0.26), residues: 353 sheet: 1.70 (0.30), residues: 240 loop : -0.39 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 96 HIS 0.005 0.001 HIS C 266 PHE 0.021 0.002 PHE C 199 TYR 0.018 0.002 TYR E 178 ARG 0.008 0.001 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.22976 ( 394) hydrogen bonds : angle 7.83157 ( 1101) SS BOND : bond 0.00847 ( 3) SS BOND : angle 1.64424 ( 6) covalent geometry : bond 0.00539 ( 8338) covalent geometry : angle 0.88430 (11338) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 142 time to evaluate : 0.896 Fit side-chains REVERT: A 113 LEU cc_start: 0.6838 (mp) cc_final: 0.6439 (mt) REVERT: B 75 GLN cc_start: 0.8059 (tt0) cc_final: 0.7812 (tt0) REVERT: C 78 LYS cc_start: 0.8356 (mttp) cc_final: 0.8009 (mttp) REVERT: C 262 MET cc_start: 0.8751 (ttm) cc_final: 0.8549 (ttm) REVERT: E 43 LYS cc_start: 0.8109 (mmtm) cc_final: 0.7790 (mmmt) outliers start: 4 outliers final: 1 residues processed: 145 average time/residue: 0.2086 time to fit residues: 40.7271 Evaluate side-chains 122 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 316 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 0.0010 chunk 42 optimal weight: 10.0000 chunk 83 optimal weight: 0.0470 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 overall best weight: 0.7486 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN C 239 ASN E 35 HIS E 167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.176060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.141277 restraints weight = 9112.387| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.79 r_work: 0.3382 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8341 Z= 0.146 Angle : 0.607 8.621 11344 Z= 0.327 Chirality : 0.044 0.180 1324 Planarity : 0.005 0.059 1425 Dihedral : 8.196 179.863 1175 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.24 % Allowed : 19.65 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.25), residues: 1052 helix: 1.27 (0.27), residues: 353 sheet: 1.48 (0.32), residues: 246 loop : -0.22 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 169 HIS 0.004 0.001 HIS E 35 PHE 0.015 0.001 PHE C 199 TYR 0.018 0.002 TYR E 178 ARG 0.004 0.000 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.04405 ( 394) hydrogen bonds : angle 4.73625 ( 1101) SS BOND : bond 0.00359 ( 3) SS BOND : angle 1.14975 ( 6) covalent geometry : bond 0.00329 ( 8338) covalent geometry : angle 0.60634 (11338) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.919 Fit side-chains REVERT: A 97 MET cc_start: 0.5237 (ppp) cc_final: 0.4461 (ppp) REVERT: A 114 MET cc_start: 0.5549 (ttp) cc_final: 0.5002 (tpt) REVERT: A 182 HIS cc_start: 0.6755 (m170) cc_final: 0.6234 (t-170) REVERT: B 75 GLN cc_start: 0.8033 (tt0) cc_final: 0.7712 (tt0) REVERT: B 147 ASP cc_start: 0.7430 (t70) cc_final: 0.7151 (m-30) REVERT: C 217 MET cc_start: 0.8534 (ptt) cc_final: 0.8256 (ptt) REVERT: C 262 MET cc_start: 0.8739 (ttm) cc_final: 0.8328 (ttm) REVERT: E 222 GLU cc_start: 0.9034 (pt0) cc_final: 0.8830 (pt0) outliers start: 19 outliers final: 11 residues processed: 152 average time/residue: 0.1959 time to fit residues: 40.7925 Evaluate side-chains 133 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 214 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 96 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 62 optimal weight: 0.4980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 ASN A 384 ASN ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.168179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.133811 restraints weight = 9476.325| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.95 r_work: 0.3267 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8341 Z= 0.190 Angle : 0.612 9.131 11344 Z= 0.327 Chirality : 0.045 0.168 1324 Planarity : 0.004 0.045 1425 Dihedral : 8.086 175.592 1174 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.88 % Allowed : 19.41 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.25), residues: 1052 helix: 1.53 (0.28), residues: 356 sheet: 1.18 (0.31), residues: 251 loop : -0.22 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 169 HIS 0.003 0.001 HIS C 311 PHE 0.021 0.002 PHE C 199 TYR 0.017 0.002 TYR E 59 ARG 0.003 0.000 ARG C 150 Details of bonding type rmsd hydrogen bonds : bond 0.04526 ( 394) hydrogen bonds : angle 4.50440 ( 1101) SS BOND : bond 0.00512 ( 3) SS BOND : angle 1.31211 ( 6) covalent geometry : bond 0.00448 ( 8338) covalent geometry : angle 0.61115 (11338) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 124 time to evaluate : 0.851 Fit side-chains REVERT: A 97 MET cc_start: 0.5065 (ppp) cc_final: 0.3789 (mmt) REVERT: A 121 MET cc_start: 0.5182 (tpt) cc_final: 0.4807 (tpp) REVERT: A 182 HIS cc_start: 0.7079 (m170) cc_final: 0.6723 (t-170) REVERT: A 245 ILE cc_start: 0.6382 (mm) cc_final: 0.6125 (mt) REVERT: B 20 ASP cc_start: 0.8114 (m-30) cc_final: 0.7862 (m-30) REVERT: B 25 GLU cc_start: 0.7265 (tm-30) cc_final: 0.6951 (mt-10) REVERT: B 75 GLN cc_start: 0.8088 (tt0) cc_final: 0.7793 (tt0) REVERT: B 222 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6336 (mt-10) REVERT: B 230 ASP cc_start: 0.7828 (m-30) cc_final: 0.7548 (m-30) REVERT: C 234 PHE cc_start: 0.8904 (OUTLIER) cc_final: 0.7930 (t80) REVERT: C 262 MET cc_start: 0.8807 (ttm) cc_final: 0.8378 (ttm) REVERT: D 42 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7164 (mp0) REVERT: E 51 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8237 (tp) outliers start: 33 outliers final: 19 residues processed: 146 average time/residue: 0.1980 time to fit residues: 39.4811 Evaluate side-chains 141 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 214 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 86 optimal weight: 0.9980 chunk 96 optimal weight: 0.0270 chunk 48 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.173111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.139411 restraints weight = 9335.291| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.74 r_work: 0.3347 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8341 Z= 0.126 Angle : 0.534 6.655 11344 Z= 0.286 Chirality : 0.042 0.158 1324 Planarity : 0.004 0.039 1425 Dihedral : 7.725 174.902 1174 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.76 % Allowed : 20.71 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.26), residues: 1052 helix: 1.98 (0.28), residues: 354 sheet: 0.99 (0.31), residues: 251 loop : -0.23 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 169 HIS 0.002 0.001 HIS C 311 PHE 0.014 0.001 PHE E 27 TYR 0.014 0.001 TYR E 178 ARG 0.002 0.000 ARG C 150 Details of bonding type rmsd hydrogen bonds : bond 0.03617 ( 394) hydrogen bonds : angle 4.21458 ( 1101) SS BOND : bond 0.00302 ( 3) SS BOND : angle 1.04228 ( 6) covalent geometry : bond 0.00288 ( 8338) covalent geometry : angle 0.53409 (11338) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 0.894 Fit side-chains REVERT: A 97 MET cc_start: 0.5198 (ppp) cc_final: 0.4078 (mmt) REVERT: A 121 MET cc_start: 0.5175 (tpt) cc_final: 0.4878 (tpp) REVERT: A 182 HIS cc_start: 0.7030 (m170) cc_final: 0.6672 (t-170) REVERT: A 208 MET cc_start: 0.4986 (ppp) cc_final: 0.4734 (ppp) REVERT: A 245 ILE cc_start: 0.6303 (mm) cc_final: 0.5937 (mt) REVERT: B 25 GLU cc_start: 0.7217 (tm-30) cc_final: 0.6937 (mt-10) REVERT: B 75 GLN cc_start: 0.8108 (tt0) cc_final: 0.7836 (tt0) REVERT: B 134 LEU cc_start: 0.8830 (mt) cc_final: 0.8607 (mp) REVERT: B 222 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6509 (mt-10) REVERT: B 230 ASP cc_start: 0.7769 (m-30) cc_final: 0.7548 (m-30) REVERT: C 234 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.7989 (t80) REVERT: D 42 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7108 (mp0) REVERT: E 51 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8051 (tp) outliers start: 32 outliers final: 24 residues processed: 149 average time/residue: 0.1934 time to fit residues: 39.6251 Evaluate side-chains 149 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 214 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 64 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 178 GLN ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.169645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.135996 restraints weight = 9345.299| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.76 r_work: 0.3297 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8341 Z= 0.144 Angle : 0.548 8.225 11344 Z= 0.292 Chirality : 0.042 0.153 1324 Planarity : 0.004 0.039 1425 Dihedral : 7.656 169.464 1174 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.35 % Allowed : 20.94 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.26), residues: 1052 helix: 2.02 (0.28), residues: 354 sheet: 0.87 (0.31), residues: 261 loop : -0.31 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 169 HIS 0.002 0.001 HIS C 142 PHE 0.016 0.001 PHE C 199 TYR 0.019 0.001 TYR E 59 ARG 0.002 0.000 ARG E 190 Details of bonding type rmsd hydrogen bonds : bond 0.03784 ( 394) hydrogen bonds : angle 4.19222 ( 1101) SS BOND : bond 0.00315 ( 3) SS BOND : angle 1.04175 ( 6) covalent geometry : bond 0.00337 ( 8338) covalent geometry : angle 0.54794 (11338) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 119 time to evaluate : 0.929 Fit side-chains REVERT: A 97 MET cc_start: 0.5125 (ppp) cc_final: 0.4743 (ppp) REVERT: A 182 HIS cc_start: 0.6991 (m170) cc_final: 0.6694 (t-170) REVERT: A 208 MET cc_start: 0.4963 (ppp) cc_final: 0.4710 (ppp) REVERT: A 245 ILE cc_start: 0.6170 (mm) cc_final: 0.5837 (mt) REVERT: B 71 GLU cc_start: 0.7704 (tt0) cc_final: 0.7366 (tt0) REVERT: B 75 GLN cc_start: 0.8134 (tt0) cc_final: 0.7849 (tt0) REVERT: B 222 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6591 (mt-10) REVERT: B 230 ASP cc_start: 0.7804 (m-30) cc_final: 0.7534 (m-30) REVERT: C 234 PHE cc_start: 0.8920 (OUTLIER) cc_final: 0.7888 (t80) REVERT: C 262 MET cc_start: 0.8831 (ttm) cc_final: 0.8611 (ttm) REVERT: D 42 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7140 (mp0) REVERT: E 51 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8118 (tp) outliers start: 37 outliers final: 27 residues processed: 145 average time/residue: 0.2006 time to fit residues: 40.0410 Evaluate side-chains 145 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 214 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 35 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 60 optimal weight: 0.2980 chunk 48 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.166970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.132269 restraints weight = 9395.116| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.18 r_work: 0.3288 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8341 Z= 0.132 Angle : 0.540 7.747 11344 Z= 0.287 Chirality : 0.042 0.152 1324 Planarity : 0.004 0.038 1425 Dihedral : 7.454 163.137 1174 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.35 % Allowed : 21.53 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.26), residues: 1052 helix: 2.11 (0.28), residues: 354 sheet: 0.73 (0.31), residues: 257 loop : -0.34 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 169 HIS 0.002 0.001 HIS C 311 PHE 0.014 0.001 PHE E 27 TYR 0.016 0.001 TYR E 59 ARG 0.002 0.000 ARG C 150 Details of bonding type rmsd hydrogen bonds : bond 0.03579 ( 394) hydrogen bonds : angle 4.10566 ( 1101) SS BOND : bond 0.00287 ( 3) SS BOND : angle 0.99316 ( 6) covalent geometry : bond 0.00305 ( 8338) covalent geometry : angle 0.54003 (11338) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 119 time to evaluate : 0.846 Fit side-chains REVERT: A 97 MET cc_start: 0.4992 (ppp) cc_final: 0.4683 (ppp) REVERT: A 182 HIS cc_start: 0.7027 (m170) cc_final: 0.6677 (t-170) REVERT: A 208 MET cc_start: 0.4911 (ppp) cc_final: 0.3858 (tpt) REVERT: A 245 ILE cc_start: 0.6135 (mm) cc_final: 0.5794 (mt) REVERT: B 25 GLU cc_start: 0.7115 (tm-30) cc_final: 0.6654 (mt-10) REVERT: B 71 GLU cc_start: 0.7803 (tt0) cc_final: 0.7432 (tp30) REVERT: B 75 GLN cc_start: 0.8145 (tt0) cc_final: 0.7844 (tt0) REVERT: B 230 ASP cc_start: 0.7848 (m-30) cc_final: 0.7581 (m-30) REVERT: C 234 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.7857 (t80) REVERT: D 42 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7164 (mp0) REVERT: E 51 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8116 (tp) outliers start: 37 outliers final: 27 residues processed: 144 average time/residue: 0.1963 time to fit residues: 38.7127 Evaluate side-chains 145 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 214 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 88 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.170964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.137376 restraints weight = 9396.193| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.78 r_work: 0.3290 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8341 Z= 0.133 Angle : 0.535 8.111 11344 Z= 0.285 Chirality : 0.042 0.151 1324 Planarity : 0.004 0.037 1425 Dihedral : 7.229 151.437 1174 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.47 % Allowed : 21.06 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.26), residues: 1052 helix: 2.15 (0.28), residues: 354 sheet: 0.67 (0.31), residues: 257 loop : -0.36 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 169 HIS 0.002 0.001 HIS C 311 PHE 0.014 0.001 PHE E 27 TYR 0.016 0.001 TYR E 59 ARG 0.002 0.000 ARG C 150 Details of bonding type rmsd hydrogen bonds : bond 0.03540 ( 394) hydrogen bonds : angle 4.08867 ( 1101) SS BOND : bond 0.00271 ( 3) SS BOND : angle 0.96220 ( 6) covalent geometry : bond 0.00309 ( 8338) covalent geometry : angle 0.53502 (11338) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 119 time to evaluate : 0.881 Fit side-chains REVERT: A 97 MET cc_start: 0.5116 (ppp) cc_final: 0.4847 (ppp) REVERT: A 182 HIS cc_start: 0.6969 (m170) cc_final: 0.6689 (t-170) REVERT: A 208 MET cc_start: 0.4960 (ppp) cc_final: 0.3898 (tpt) REVERT: A 245 ILE cc_start: 0.6059 (mm) cc_final: 0.5721 (mt) REVERT: B 9 ASP cc_start: 0.8127 (t0) cc_final: 0.7921 (m-30) REVERT: B 25 GLU cc_start: 0.7132 (tm-30) cc_final: 0.6717 (mt-10) REVERT: B 71 GLU cc_start: 0.7836 (tt0) cc_final: 0.7523 (tp30) REVERT: B 75 GLN cc_start: 0.8147 (tt0) cc_final: 0.7864 (tt0) REVERT: B 230 ASP cc_start: 0.7784 (m-30) cc_final: 0.7548 (m-30) REVERT: C 25 CYS cc_start: 0.6920 (m) cc_final: 0.6384 (p) REVERT: C 234 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.7861 (t80) REVERT: C 262 MET cc_start: 0.8841 (ttm) cc_final: 0.8441 (ttm) REVERT: D 42 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7113 (mp0) REVERT: E 51 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8066 (tp) outliers start: 38 outliers final: 26 residues processed: 145 average time/residue: 0.1931 time to fit residues: 38.5306 Evaluate side-chains 145 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 214 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 88 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 62 optimal weight: 0.0050 chunk 61 optimal weight: 1.9990 chunk 54 optimal weight: 0.0980 chunk 35 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.173592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.139815 restraints weight = 9399.817| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.71 r_work: 0.3364 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8341 Z= 0.111 Angle : 0.518 8.849 11344 Z= 0.274 Chirality : 0.041 0.150 1324 Planarity : 0.004 0.036 1425 Dihedral : 6.798 136.273 1174 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.41 % Allowed : 22.35 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.26), residues: 1052 helix: 2.33 (0.28), residues: 352 sheet: 0.64 (0.31), residues: 257 loop : -0.34 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 169 HIS 0.002 0.001 HIS C 311 PHE 0.013 0.001 PHE E 27 TYR 0.014 0.001 TYR E 59 ARG 0.002 0.000 ARG C 214 Details of bonding type rmsd hydrogen bonds : bond 0.03258 ( 394) hydrogen bonds : angle 3.97709 ( 1101) SS BOND : bond 0.00252 ( 3) SS BOND : angle 0.90395 ( 6) covalent geometry : bond 0.00248 ( 8338) covalent geometry : angle 0.51755 (11338) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 1.009 Fit side-chains REVERT: A 97 MET cc_start: 0.5152 (ppp) cc_final: 0.4821 (ppp) REVERT: A 182 HIS cc_start: 0.6909 (m170) cc_final: 0.6671 (t70) REVERT: A 208 MET cc_start: 0.5053 (ppp) cc_final: 0.3987 (tpt) REVERT: A 245 ILE cc_start: 0.6120 (mm) cc_final: 0.5755 (mt) REVERT: B 24 ARG cc_start: 0.7609 (mtm-85) cc_final: 0.7108 (mtm110) REVERT: B 25 GLU cc_start: 0.7186 (tm-30) cc_final: 0.6814 (mt-10) REVERT: B 71 GLU cc_start: 0.7705 (tt0) cc_final: 0.7404 (tt0) REVERT: B 75 GLN cc_start: 0.8129 (tt0) cc_final: 0.7869 (tt0) REVERT: B 230 ASP cc_start: 0.7706 (m-30) cc_final: 0.7500 (m-30) REVERT: C 234 PHE cc_start: 0.8916 (OUTLIER) cc_final: 0.7881 (t80) REVERT: D 42 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7071 (mp0) REVERT: E 51 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.7982 (tp) outliers start: 29 outliers final: 21 residues processed: 140 average time/residue: 0.2121 time to fit residues: 39.9327 Evaluate side-chains 138 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 203 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 4 optimal weight: 7.9990 chunk 35 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 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 110 ASN ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.171380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.137328 restraints weight = 9582.019| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.82 r_work: 0.3279 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8341 Z= 0.145 Angle : 0.546 8.684 11344 Z= 0.289 Chirality : 0.042 0.150 1324 Planarity : 0.004 0.036 1425 Dihedral : 6.808 123.225 1174 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.06 % Allowed : 22.24 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.26), residues: 1052 helix: 2.23 (0.28), residues: 353 sheet: 0.64 (0.31), residues: 256 loop : -0.40 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 169 HIS 0.002 0.001 HIS C 311 PHE 0.014 0.001 PHE C 199 TYR 0.017 0.001 TYR E 59 ARG 0.002 0.000 ARG E 190 Details of bonding type rmsd hydrogen bonds : bond 0.03566 ( 394) hydrogen bonds : angle 4.04130 ( 1101) SS BOND : bond 0.00277 ( 3) SS BOND : angle 0.93536 ( 6) covalent geometry : bond 0.00343 ( 8338) covalent geometry : angle 0.54587 (11338) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.880 Fit side-chains REVERT: A 97 MET cc_start: 0.5155 (ppp) cc_final: 0.4846 (ppp) REVERT: A 208 MET cc_start: 0.5005 (ppp) cc_final: 0.3895 (tpt) REVERT: A 245 ILE cc_start: 0.6051 (mm) cc_final: 0.5724 (mt) REVERT: B 25 GLU cc_start: 0.7241 (tm-30) cc_final: 0.6869 (mt-10) REVERT: B 71 GLU cc_start: 0.7885 (tt0) cc_final: 0.7407 (tt0) REVERT: B 75 GLN cc_start: 0.8137 (tt0) cc_final: 0.7863 (tt0) REVERT: B 230 ASP cc_start: 0.7746 (m-30) cc_final: 0.7468 (m-30) REVERT: C 25 CYS cc_start: 0.6858 (m) cc_final: 0.6420 (p) REVERT: C 234 PHE cc_start: 0.8924 (OUTLIER) cc_final: 0.7799 (t80) REVERT: C 262 MET cc_start: 0.8821 (ttm) cc_final: 0.8525 (ttm) REVERT: D 42 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7096 (mp0) REVERT: E 51 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8085 (tp) outliers start: 26 outliers final: 22 residues processed: 135 average time/residue: 0.2004 time to fit residues: 36.9340 Evaluate side-chains 143 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 203 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 1 optimal weight: 0.0770 chunk 99 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.172028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.138235 restraints weight = 9430.746| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.74 r_work: 0.3328 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8341 Z= 0.126 Angle : 0.531 8.892 11344 Z= 0.281 Chirality : 0.042 0.151 1324 Planarity : 0.004 0.036 1425 Dihedral : 6.753 121.989 1174 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.71 % Allowed : 22.71 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.26), residues: 1052 helix: 2.27 (0.28), residues: 353 sheet: 0.63 (0.31), residues: 256 loop : -0.41 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 169 HIS 0.002 0.001 HIS C 311 PHE 0.013 0.001 PHE E 27 TYR 0.016 0.001 TYR E 59 ARG 0.002 0.000 ARG E 190 Details of bonding type rmsd hydrogen bonds : bond 0.03414 ( 394) hydrogen bonds : angle 4.00012 ( 1101) SS BOND : bond 0.00255 ( 3) SS BOND : angle 0.89750 ( 6) covalent geometry : bond 0.00291 ( 8338) covalent geometry : angle 0.53030 (11338) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.896 Fit side-chains REVERT: A 97 MET cc_start: 0.5140 (ppp) cc_final: 0.4822 (ppp) REVERT: A 208 MET cc_start: 0.4988 (ppp) cc_final: 0.3896 (tpt) REVERT: A 245 ILE cc_start: 0.5937 (mm) cc_final: 0.5593 (mt) REVERT: B 25 GLU cc_start: 0.7204 (tm-30) cc_final: 0.6853 (mt-10) REVERT: B 71 GLU cc_start: 0.7848 (tt0) cc_final: 0.7459 (tt0) REVERT: B 75 GLN cc_start: 0.8125 (tt0) cc_final: 0.7850 (tt0) REVERT: B 230 ASP cc_start: 0.7724 (m-30) cc_final: 0.7477 (m-30) REVERT: C 234 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.7800 (t80) REVERT: C 262 MET cc_start: 0.8832 (ttm) cc_final: 0.8530 (ttm) REVERT: D 42 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7082 (mp0) REVERT: E 51 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8057 (tp) outliers start: 23 outliers final: 20 residues processed: 136 average time/residue: 0.1995 time to fit residues: 37.1352 Evaluate side-chains 143 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 238 MET Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 203 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 104 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 42 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 88 optimal weight: 0.4980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.170720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.137205 restraints weight = 9548.243| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.77 r_work: 0.3314 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8341 Z= 0.155 Angle : 0.557 9.022 11344 Z= 0.294 Chirality : 0.042 0.151 1324 Planarity : 0.004 0.036 1425 Dihedral : 6.793 120.292 1174 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.06 % Allowed : 22.47 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.26), residues: 1052 helix: 2.17 (0.28), residues: 352 sheet: 0.65 (0.31), residues: 262 loop : -0.45 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 169 HIS 0.003 0.001 HIS C 311 PHE 0.016 0.001 PHE C 199 TYR 0.017 0.001 TYR E 59 ARG 0.005 0.000 ARG C 214 Details of bonding type rmsd hydrogen bonds : bond 0.03638 ( 394) hydrogen bonds : angle 4.05461 ( 1101) SS BOND : bond 0.00272 ( 3) SS BOND : angle 0.92457 ( 6) covalent geometry : bond 0.00367 ( 8338) covalent geometry : angle 0.55723 (11338) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4918.74 seconds wall clock time: 85 minutes 46.42 seconds (5146.42 seconds total)