Starting phenix.real_space_refine on Wed Sep 17 10:38:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9as4_43804/09_2025/9as4_43804.cif Found real_map, /net/cci-nas-00/data/ceres_data/9as4_43804/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9as4_43804/09_2025/9as4_43804.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9as4_43804/09_2025/9as4_43804.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9as4_43804/09_2025/9as4_43804.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9as4_43804/09_2025/9as4_43804.map" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ARG:plan': 4, 'ASN:plan1': 2, 'PHE:plan': 2, 'ASP:plan': 4, 'GLN:plan1': 1, 'GLU:plan': 1} 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: {'GLU:plan': 3, 'ARG:plan': 6, 'GLN:plan1': 1, '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: {'GLU:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP: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: {'ARG:plan': 1, 'GLU:plan': 2, '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: {'GLU:plan': 6, 'GLN:plan1': 1, '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: 2.30, per 1000 atoms: 0.28 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: 0.72 Conformation dependent library (CDL) restraints added in 518.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.31 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: 1.34 Time building geometry restraints manager: 0.99 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: 3.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.350 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.380 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.001 ARG B 35 TYR 0.018 0.002 TYR E 178 PHE 0.021 0.002 PHE C 199 TRP 0.026 0.002 TRP B 96 HIS 0.005 0.001 HIS C 266 Details of bonding type rmsd covalent geometry : bond 0.00539 ( 8338) covalent geometry : angle 0.88430 (11338) SS BOND : bond 0.00847 ( 3) SS BOND : angle 1.64424 ( 6) hydrogen bonds : bond 0.22976 ( 394) hydrogen bonds : angle 7.83157 ( 1101) *********************** 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 : 0.312 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: 0.0926 time to fit residues: 18.2076 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 : 0.368 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3940 r_free = 0.3940 target = 0.176274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.141262 restraints weight = 9223.921| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.79 r_work: 0.3380 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8341 Z= 0.146 Angle : 0.604 8.486 11344 Z= 0.325 Chirality : 0.044 0.178 1324 Planarity : 0.005 0.060 1425 Dihedral : 8.188 179.814 1175 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.11 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.25), residues: 1052 helix: 1.26 (0.27), residues: 353 sheet: 1.49 (0.32), residues: 246 loop : -0.22 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 35 TYR 0.018 0.002 TYR E 178 PHE 0.015 0.001 PHE C 199 TRP 0.020 0.002 TRP C 169 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8338) covalent geometry : angle 0.60385 (11338) SS BOND : bond 0.00364 ( 3) SS BOND : angle 1.18671 ( 6) hydrogen bonds : bond 0.04378 ( 394) hydrogen bonds : angle 4.72993 ( 1101) *********************** 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 158 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: A 97 MET cc_start: 0.5240 (ppp) cc_final: 0.4473 (ppp) REVERT: A 110 ASN cc_start: 0.6130 (OUTLIER) cc_final: 0.5917 (t0) REVERT: A 114 MET cc_start: 0.5542 (ttp) cc_final: 0.5013 (tpt) REVERT: A 179 ASN cc_start: 0.7759 (p0) cc_final: 0.7546 (p0) REVERT: A 182 HIS cc_start: 0.6751 (m170) cc_final: 0.6220 (t-170) REVERT: B 75 GLN cc_start: 0.8081 (tt0) cc_final: 0.7770 (tt0) REVERT: C 217 MET cc_start: 0.8511 (ptt) cc_final: 0.8228 (ptt) REVERT: C 262 MET cc_start: 0.8757 (ttm) cc_final: 0.8340 (ttm) REVERT: E 222 GLU cc_start: 0.9039 (pt0) cc_final: 0.8836 (pt0) outliers start: 19 outliers final: 11 residues processed: 150 average time/residue: 0.0823 time to fit residues: 16.9978 Evaluate side-chains 134 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 181 ILE 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 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 47 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 42 optimal weight: 0.3980 chunk 29 optimal weight: 0.0670 chunk 39 optimal weight: 0.0770 chunk 24 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 376 ASN A 384 ASN ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.178601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.144114 restraints weight = 9262.424| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.83 r_work: 0.3399 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8341 Z= 0.106 Angle : 0.525 5.810 11344 Z= 0.282 Chirality : 0.042 0.156 1324 Planarity : 0.004 0.041 1425 Dihedral : 7.585 175.640 1174 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.82 % Allowed : 20.24 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.26), residues: 1052 helix: 1.86 (0.28), residues: 355 sheet: 1.33 (0.32), residues: 251 loop : -0.17 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 42 TYR 0.015 0.001 TYR E 178 PHE 0.013 0.001 PHE E 27 TRP 0.017 0.001 TRP C 169 HIS 0.002 0.001 HIS C 91 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 8338) covalent geometry : angle 0.52411 (11338) SS BOND : bond 0.00424 ( 3) SS BOND : angle 1.22514 ( 6) hydrogen bonds : bond 0.03598 ( 394) hydrogen bonds : angle 4.21724 ( 1101) *********************** 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 159 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.311 Fit side-chains REVERT: A 97 MET cc_start: 0.4994 (ppp) cc_final: 0.3719 (mmt) REVERT: A 121 MET cc_start: 0.5198 (tpt) cc_final: 0.4752 (tpp) REVERT: A 182 HIS cc_start: 0.6832 (m170) cc_final: 0.6463 (t-170) REVERT: A 317 ASN cc_start: 0.5946 (m110) cc_final: 0.5683 (m-40) REVERT: B 25 GLU cc_start: 0.7288 (tm-30) cc_final: 0.6984 (mt-10) REVERT: B 75 GLN cc_start: 0.7971 (tt0) cc_final: 0.7715 (tt0) REVERT: B 134 LEU cc_start: 0.8800 (mt) cc_final: 0.8566 (mp) REVERT: B 222 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.6321 (mt-10) REVERT: C 217 MET cc_start: 0.8565 (ptt) cc_final: 0.8296 (ptt) REVERT: C 234 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.7933 (t80) REVERT: C 246 ASP cc_start: 0.8304 (m-30) cc_final: 0.8059 (m-30) REVERT: C 262 MET cc_start: 0.8661 (ttm) cc_final: 0.8373 (ttm) outliers start: 24 outliers final: 15 residues processed: 150 average time/residue: 0.0923 time to fit residues: 18.8205 Evaluate side-chains 140 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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 B residue 76 VAL 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 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 E residue 22 CYS 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 73 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 38 optimal weight: 0.0170 overall best weight: 1.1822 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.169344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.134925 restraints weight = 9479.249| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.84 r_work: 0.3309 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8341 Z= 0.176 Angle : 0.586 9.388 11344 Z= 0.311 Chirality : 0.043 0.169 1324 Planarity : 0.004 0.043 1425 Dihedral : 7.978 179.420 1174 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.65 % Allowed : 21.18 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.26), residues: 1052 helix: 1.93 (0.28), residues: 354 sheet: 1.09 (0.31), residues: 258 loop : -0.19 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 190 TYR 0.012 0.001 TYR E 178 PHE 0.020 0.002 PHE C 199 TRP 0.015 0.002 TRP C 169 HIS 0.003 0.001 HIS C 142 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 8338) covalent geometry : angle 0.58545 (11338) SS BOND : bond 0.00375 ( 3) SS BOND : angle 1.14719 ( 6) hydrogen bonds : bond 0.04106 ( 394) hydrogen bonds : angle 4.28291 ( 1101) *********************** 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 155 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 0.270 Fit side-chains REVERT: A 97 MET cc_start: 0.5210 (ppp) cc_final: 0.4082 (mmt) REVERT: A 121 MET cc_start: 0.5047 (tpt) cc_final: 0.4698 (tpp) REVERT: A 182 HIS cc_start: 0.7102 (m170) cc_final: 0.6690 (t-170) REVERT: A 208 MET cc_start: 0.4912 (ppp) cc_final: 0.4694 (ppp) REVERT: A 245 ILE cc_start: 0.6297 (mm) cc_final: 0.5993 (mt) REVERT: B 25 GLU cc_start: 0.7185 (tm-30) cc_final: 0.6960 (tm-30) REVERT: B 71 GLU cc_start: 0.7679 (tt0) cc_final: 0.7365 (tt0) REVERT: B 75 GLN cc_start: 0.8081 (tt0) cc_final: 0.7804 (tt0) REVERT: B 222 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6517 (mt-10) REVERT: B 230 ASP cc_start: 0.7721 (m-30) cc_final: 0.7430 (m-30) REVERT: C 234 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.7937 (t80) REVERT: C 246 ASP cc_start: 0.8357 (m-30) cc_final: 0.7975 (m-30) REVERT: D 42 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.6999 (mp0) REVERT: E 51 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8231 (tp) outliers start: 31 outliers final: 22 residues processed: 142 average time/residue: 0.0926 time to fit residues: 18.0452 Evaluate side-chains 145 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 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 263 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 35 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 70 optimal weight: 0.2980 chunk 73 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN ** 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 = 0.3892 r_free = 0.3892 target = 0.171578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.137879 restraints weight = 9439.356| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.72 r_work: 0.3328 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8341 Z= 0.154 Angle : 0.557 7.944 11344 Z= 0.296 Chirality : 0.042 0.161 1324 Planarity : 0.004 0.041 1425 Dihedral : 7.894 179.436 1174 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.00 % Allowed : 20.35 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.25), residues: 1052 helix: 1.99 (0.28), residues: 354 sheet: 0.91 (0.31), residues: 263 loop : -0.30 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 150 TYR 0.014 0.001 TYR E 178 PHE 0.016 0.001 PHE C 199 TRP 0.015 0.002 TRP C 169 HIS 0.003 0.001 HIS C 311 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 8338) covalent geometry : angle 0.55645 (11338) SS BOND : bond 0.00341 ( 3) SS BOND : angle 1.10123 ( 6) hydrogen bonds : bond 0.03799 ( 394) hydrogen bonds : angle 4.19091 ( 1101) *********************** 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 161 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 0.307 Fit side-chains REVERT: A 97 MET cc_start: 0.5182 (ppp) cc_final: 0.4213 (mmt) REVERT: A 182 HIS cc_start: 0.6888 (m170) cc_final: 0.6627 (t-170) REVERT: A 208 MET cc_start: 0.4948 (ppp) cc_final: 0.4684 (ppp) REVERT: A 245 ILE cc_start: 0.6234 (mm) cc_final: 0.5919 (mt) REVERT: B 9 ASP cc_start: 0.8118 (t0) cc_final: 0.7914 (m-30) REVERT: B 20 ASP cc_start: 0.8059 (m-30) cc_final: 0.7799 (m-30) REVERT: B 71 GLU cc_start: 0.7773 (tt0) cc_final: 0.7311 (tt0) REVERT: B 222 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6558 (mt-10) REVERT: B 230 ASP cc_start: 0.7741 (m-30) cc_final: 0.7458 (m-30) REVERT: C 234 PHE cc_start: 0.8893 (OUTLIER) cc_final: 0.7865 (t80) REVERT: C 246 ASP cc_start: 0.8253 (m-30) cc_final: 0.7925 (m-30) REVERT: C 262 MET cc_start: 0.8819 (ttm) cc_final: 0.8597 (ttm) REVERT: D 42 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7148 (mp0) REVERT: E 51 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8156 (tp) outliers start: 34 outliers final: 23 residues processed: 148 average time/residue: 0.0895 time to fit residues: 18.2871 Evaluate side-chains 147 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 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 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 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 27 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 10 optimal weight: 0.0870 chunk 57 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN ** 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 = 0.3879 r_free = 0.3879 target = 0.170497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.137104 restraints weight = 9331.010| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.83 r_work: 0.3310 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3119 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= 0.124 Angle : 0.531 7.282 11344 Z= 0.283 Chirality : 0.042 0.152 1324 Planarity : 0.004 0.037 1425 Dihedral : 7.684 178.363 1174 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.12 % Allowed : 20.59 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.26), residues: 1052 helix: 2.11 (0.28), residues: 355 sheet: 0.88 (0.31), residues: 262 loop : -0.37 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 190 TYR 0.015 0.001 TYR E 59 PHE 0.014 0.001 PHE E 27 TRP 0.016 0.001 TRP C 169 HIS 0.002 0.001 HIS C 311 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8338) covalent geometry : angle 0.53071 (11338) SS BOND : bond 0.00291 ( 3) SS BOND : angle 1.00972 ( 6) hydrogen bonds : bond 0.03481 ( 394) hydrogen bonds : angle 4.05905 ( 1101) *********************** 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 161 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 126 time to evaluate : 0.304 Fit side-chains REVERT: A 97 MET cc_start: 0.5090 (ppp) cc_final: 0.4758 (ppp) REVERT: A 182 HIS cc_start: 0.6914 (m170) cc_final: 0.6601 (t-170) REVERT: A 208 MET cc_start: 0.4934 (ppp) cc_final: 0.3904 (tpt) REVERT: A 245 ILE cc_start: 0.5999 (mm) cc_final: 0.5636 (mt) REVERT: B 25 GLU cc_start: 0.7136 (tm-30) cc_final: 0.6674 (mt-10) REVERT: B 71 GLU cc_start: 0.7745 (tt0) cc_final: 0.7481 (tt0) REVERT: B 75 GLN cc_start: 0.8028 (tt0) cc_final: 0.7758 (tt0) REVERT: B 230 ASP cc_start: 0.7768 (m-30) cc_final: 0.7494 (m-30) REVERT: C 234 PHE cc_start: 0.8901 (OUTLIER) cc_final: 0.7916 (t80) REVERT: C 262 MET cc_start: 0.8859 (ttm) cc_final: 0.8471 (ttm) REVERT: D 42 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7103 (mp0) REVERT: E 51 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8124 (tp) outliers start: 35 outliers final: 23 residues processed: 149 average time/residue: 0.0927 time to fit residues: 18.9109 Evaluate side-chains 141 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 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 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 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 48 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 44 optimal weight: 0.0030 chunk 39 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 58 optimal weight: 0.0870 chunk 94 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.6570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN ** 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 = 0.3888 r_free = 0.3888 target = 0.171384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.137470 restraints weight = 9549.259| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.87 r_work: 0.3321 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8341 Z= 0.121 Angle : 0.525 7.559 11344 Z= 0.278 Chirality : 0.041 0.150 1324 Planarity : 0.004 0.037 1425 Dihedral : 7.493 174.028 1174 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.88 % Allowed : 20.35 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.26), residues: 1052 helix: 2.16 (0.28), residues: 355 sheet: 0.77 (0.31), residues: 257 loop : -0.36 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 214 TYR 0.016 0.001 TYR E 59 PHE 0.014 0.001 PHE E 27 TRP 0.015 0.001 TRP C 169 HIS 0.002 0.001 HIS C 311 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8338) covalent geometry : angle 0.52451 (11338) SS BOND : bond 0.00277 ( 3) SS BOND : angle 0.97848 ( 6) hydrogen bonds : bond 0.03363 ( 394) hydrogen bonds : angle 4.00973 ( 1101) *********************** 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 155 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 122 time to evaluate : 0.309 Fit side-chains REVERT: A 97 MET cc_start: 0.5045 (ppp) cc_final: 0.4732 (ppp) REVERT: A 182 HIS cc_start: 0.6940 (m170) cc_final: 0.6583 (t-170) REVERT: A 208 MET cc_start: 0.4954 (ppp) cc_final: 0.3907 (tpt) REVERT: A 245 ILE cc_start: 0.6116 (mm) cc_final: 0.5812 (mt) REVERT: B 25 GLU cc_start: 0.7180 (tm-30) cc_final: 0.6765 (mt-10) REVERT: B 71 GLU cc_start: 0.7774 (tt0) cc_final: 0.7496 (tt0) REVERT: B 75 GLN cc_start: 0.8077 (tt0) cc_final: 0.7795 (tt0) REVERT: B 83 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8151 (ttp) REVERT: B 230 ASP cc_start: 0.7744 (m-30) cc_final: 0.7511 (m-30) REVERT: C 234 PHE cc_start: 0.8901 (OUTLIER) cc_final: 0.7854 (t80) REVERT: C 262 MET cc_start: 0.8830 (ttm) cc_final: 0.8444 (ttm) REVERT: D 42 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7104 (mp0) REVERT: E 51 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8090 (tp) outliers start: 33 outliers final: 24 residues processed: 143 average time/residue: 0.0918 time to fit residues: 18.0282 Evaluate side-chains 147 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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 83 MET 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 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 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 5 optimal weight: 0.9980 chunk 31 optimal weight: 0.0470 chunk 4 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- 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** C 155 ASN D 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.171438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.137838 restraints weight = 9444.353| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.74 r_work: 0.3292 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3335 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 : 0.544 8.491 11344 Z= 0.288 Chirality : 0.042 0.153 1324 Planarity : 0.004 0.036 1425 Dihedral : 7.518 170.946 1174 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.29 % Allowed : 21.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.26), residues: 1052 helix: 2.12 (0.28), residues: 355 sheet: 0.74 (0.31), residues: 257 loop : -0.41 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 150 TYR 0.017 0.001 TYR E 59 PHE 0.016 0.001 PHE C 199 TRP 0.014 0.001 TRP C 169 HIS 0.002 0.001 HIS C 311 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 8338) covalent geometry : angle 0.54352 (11338) SS BOND : bond 0.00293 ( 3) SS BOND : angle 0.98643 ( 6) hydrogen bonds : bond 0.03568 ( 394) hydrogen bonds : angle 4.04256 ( 1101) *********************** 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 151 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.331 Fit side-chains REVERT: A 97 MET cc_start: 0.5151 (ppp) cc_final: 0.4773 (ppp) REVERT: A 182 HIS cc_start: 0.7028 (m170) cc_final: 0.6782 (t-170) REVERT: A 186 PHE cc_start: 0.4952 (OUTLIER) cc_final: 0.4737 (m-80) REVERT: A 208 MET cc_start: 0.4960 (ppp) cc_final: 0.3942 (tpt) REVERT: A 245 ILE cc_start: 0.5966 (mm) cc_final: 0.5632 (mt) REVERT: B 25 GLU cc_start: 0.7235 (tm-30) cc_final: 0.6827 (mt-10) REVERT: B 71 GLU cc_start: 0.7795 (tt0) cc_final: 0.7192 (tt0) REVERT: B 75 GLN cc_start: 0.8065 (tt0) cc_final: 0.7800 (tt0) REVERT: B 230 ASP cc_start: 0.7808 (m-30) cc_final: 0.7490 (m-30) REVERT: C 25 CYS cc_start: 0.6941 (m) cc_final: 0.6474 (p) REVERT: C 234 PHE cc_start: 0.8918 (OUTLIER) cc_final: 0.7779 (t80) REVERT: C 262 MET cc_start: 0.8824 (ttm) cc_final: 0.8425 (ttm) REVERT: D 42 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7150 (mp0) REVERT: E 51 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8118 (tp) outliers start: 28 outliers final: 23 residues processed: 142 average time/residue: 0.0934 time to fit residues: 18.2149 Evaluate side-chains 149 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 PHE 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 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 181 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 196 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 203 THR Chi-restraints excluded: chain E residue 214 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3887 r_free = 0.3887 target = 0.171014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.136791 restraints weight = 9396.957| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.74 r_work: 0.3255 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8341 Z= 0.151 Angle : 0.553 8.768 11344 Z= 0.292 Chirality : 0.042 0.155 1324 Planarity : 0.004 0.037 1425 Dihedral : 7.533 168.265 1174 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.53 % Allowed : 21.06 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.26), residues: 1052 helix: 2.08 (0.28), residues: 356 sheet: 0.69 (0.31), residues: 262 loop : -0.41 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 150 TYR 0.017 0.001 TYR E 59 PHE 0.015 0.001 PHE C 199 TRP 0.014 0.001 TRP C 169 HIS 0.003 0.001 HIS C 311 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 8338) covalent geometry : angle 0.55280 (11338) SS BOND : bond 0.00302 ( 3) SS BOND : angle 0.98695 ( 6) hydrogen bonds : bond 0.03617 ( 394) hydrogen bonds : angle 4.06607 ( 1101) *********************** 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 154 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.346 Fit side-chains REVERT: A 97 MET cc_start: 0.5144 (ppp) cc_final: 0.4792 (ppp) REVERT: A 182 HIS cc_start: 0.6969 (m170) cc_final: 0.6724 (t-170) REVERT: A 186 PHE cc_start: 0.4945 (OUTLIER) cc_final: 0.4709 (m-80) REVERT: A 208 MET cc_start: 0.4990 (ppp) cc_final: 0.3975 (tpt) REVERT: A 245 ILE cc_start: 0.6004 (mm) cc_final: 0.5676 (mt) REVERT: B 25 GLU cc_start: 0.7122 (tm-30) cc_final: 0.6683 (mt-10) REVERT: B 71 GLU cc_start: 0.7927 (tt0) cc_final: 0.7250 (tt0) REVERT: B 75 GLN cc_start: 0.8059 (tt0) cc_final: 0.7782 (tt0) REVERT: B 83 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8168 (ttp) REVERT: B 230 ASP cc_start: 0.7804 (m-30) cc_final: 0.7476 (m-30) REVERT: C 25 CYS cc_start: 0.6860 (m) cc_final: 0.6359 (p) REVERT: C 234 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.7765 (t80) REVERT: D 42 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7147 (mp0) REVERT: E 51 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8144 (tp) outliers start: 30 outliers final: 24 residues processed: 142 average time/residue: 0.0954 time to fit residues: 18.5609 Evaluate side-chains 152 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 PHE 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 83 MET 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 203 THR Chi-restraints excluded: chain E residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 72 optimal weight: 0.4980 chunk 5 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 29 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 65 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3914 r_free = 0.3914 target = 0.173625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.139779 restraints weight = 9394.505| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.75 r_work: 0.3302 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8341 Z= 0.112 Angle : 0.514 8.931 11344 Z= 0.273 Chirality : 0.041 0.150 1324 Planarity : 0.004 0.037 1425 Dihedral : 7.232 165.509 1174 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.94 % Allowed : 21.76 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.26), residues: 1052 helix: 2.32 (0.28), residues: 353 sheet: 0.77 (0.31), residues: 259 loop : -0.37 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 214 TYR 0.015 0.001 TYR E 59 PHE 0.014 0.001 PHE E 27 TRP 0.014 0.001 TRP C 169 HIS 0.002 0.001 HIS C 311 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 8338) covalent geometry : angle 0.51398 (11338) SS BOND : bond 0.00246 ( 3) SS BOND : angle 0.88282 ( 6) hydrogen bonds : bond 0.03184 ( 394) hydrogen bonds : angle 3.92064 ( 1101) ********************** 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 150 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.381 Fit side-chains REVERT: A 97 MET cc_start: 0.5307 (ppp) cc_final: 0.4962 (ppp) REVERT: A 182 HIS cc_start: 0.7009 (m170) cc_final: 0.6685 (t-170) REVERT: A 186 PHE cc_start: 0.5136 (OUTLIER) cc_final: 0.4711 (m-80) REVERT: A 208 MET cc_start: 0.5004 (ppp) cc_final: 0.4006 (tpt) REVERT: A 245 ILE cc_start: 0.5856 (mm) cc_final: 0.5486 (mt) REVERT: B 25 GLU cc_start: 0.7142 (tm-30) cc_final: 0.6725 (mt-10) REVERT: B 71 GLU cc_start: 0.7748 (tt0) cc_final: 0.7438 (tp30) REVERT: B 75 GLN cc_start: 0.8082 (tt0) cc_final: 0.7791 (tt0) REVERT: B 83 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8113 (ttp) REVERT: B 230 ASP cc_start: 0.7705 (m-30) cc_final: 0.7400 (m-30) REVERT: C 25 CYS cc_start: 0.6666 (m) cc_final: 0.6380 (p) REVERT: C 234 PHE cc_start: 0.8920 (OUTLIER) cc_final: 0.7773 (t80) REVERT: D 42 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7074 (mp0) REVERT: E 51 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8033 (tp) outliers start: 25 outliers final: 20 residues processed: 140 average time/residue: 0.0975 time to fit residues: 18.6995 Evaluate side-chains 149 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 PHE 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 83 MET 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 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 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 66 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 chunk 71 optimal weight: 0.0370 chunk 5 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.9664 ------------------------------------------------------------------------------- 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** C 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.171462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.137513 restraints weight = 9426.774| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.85 r_work: 0.3271 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8341 Z= 0.150 Angle : 0.550 8.798 11344 Z= 0.291 Chirality : 0.042 0.152 1324 Planarity : 0.004 0.037 1425 Dihedral : 7.419 166.518 1174 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.41 % Allowed : 21.41 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.26), residues: 1052 helix: 2.19 (0.28), residues: 355 sheet: 0.69 (0.31), residues: 264 loop : -0.46 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 148 TYR 0.017 0.001 TYR E 59 PHE 0.016 0.001 PHE C 199 TRP 0.014 0.001 TRP C 169 HIS 0.003 0.001 HIS C 311 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 8338) covalent geometry : angle 0.54931 (11338) SS BOND : bond 0.00279 ( 3) SS BOND : angle 0.97606 ( 6) hydrogen bonds : bond 0.03566 ( 394) hydrogen bonds : angle 4.04353 ( 1101) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2570.09 seconds wall clock time: 44 minutes 44.90 seconds (2684.90 seconds total)