Starting phenix.real_space_refine on Sun Dec 29 03:42:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yjh_39342/12_2024/8yjh_39342.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yjh_39342/12_2024/8yjh_39342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yjh_39342/12_2024/8yjh_39342.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yjh_39342/12_2024/8yjh_39342.map" model { file = "/net/cci-nas-00/data/ceres_data/8yjh_39342/12_2024/8yjh_39342.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yjh_39342/12_2024/8yjh_39342.cif" } resolution = 3.68 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 55 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 53 5.49 5 S 63 5.16 5 C 5965 2.51 5 N 1631 2.21 5 O 2023 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 9735 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 1963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1963 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 7, 'TRANS': 247} Chain: "C" Number of atoms: 1963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1963 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 7, 'TRANS': 247} Chain: "A" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1955 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain: "D" Number of atoms: 2769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2769 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 15, 'TRANS': 335} Chain: "J" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 308 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "E" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 512 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "F" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 205 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "H" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Classifications: {'DNA': 3} Link IDs: {'rna3p': 2} Time building chain proxies: 6.87, per 1000 atoms: 0.71 Number of scatterers: 9735 At special positions: 0 Unit cell: (106.24, 95.45, 101.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 P 53 15.00 O 2023 8.00 N 1631 7.00 C 5965 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 162 " 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: 2.48 Conformation dependent library (CDL) restraints added in 1.0 seconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2106 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 10 sheets defined 28.9% alpha, 25.4% beta 14 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 3.69 Creating SS restraints... Processing helix chain 'B' and resid 8 through 19 removed outlier: 4.262A pdb=" N LEU B 12 " --> pdb=" O GLN B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 81 Processing helix chain 'B' and resid 141 through 152 Processing helix chain 'B' and resid 209 through 217 Processing helix chain 'B' and resid 218 through 222 removed outlier: 3.975A pdb=" N LEU B 221 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER B 222 " --> pdb=" O THR B 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 218 through 222' Processing helix chain 'C' and resid 9 through 20 removed outlier: 3.729A pdb=" N LYS C 13 " --> pdb=" O GLY C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 141 through 153 Processing helix chain 'C' and resid 209 through 217 Processing helix chain 'C' and resid 218 through 222 removed outlier: 3.528A pdb=" N LEU C 221 " --> pdb=" O ALA C 218 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER C 222 " --> pdb=" O THR C 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 218 through 222' Processing helix chain 'A' and resid 8 through 19 removed outlier: 4.365A pdb=" N LEU A 12 " --> pdb=" O GLN A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 141 through 152 Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'D' and resid 5 through 14 Processing helix chain 'D' and resid 35 through 45 removed outlier: 3.744A pdb=" N ALA D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 76 Processing helix chain 'D' and resid 93 through 118 removed outlier: 3.711A pdb=" N GLN D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN D 113 " --> pdb=" O LYS D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 128 Processing helix chain 'D' and resid 134 through 149 removed outlier: 3.561A pdb=" N GLY D 149 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 169 removed outlier: 3.767A pdb=" N SER D 162 " --> pdb=" O GLU D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 185 removed outlier: 3.967A pdb=" N THR D 184 " --> pdb=" O MET D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 216 Processing helix chain 'D' and resid 219 through 231 Processing helix chain 'D' and resid 242 through 252 removed outlier: 3.650A pdb=" N VAL D 247 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASP D 248 " --> pdb=" O LYS D 244 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS D 252 " --> pdb=" O ASP D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 263 removed outlier: 3.744A pdb=" N ILE D 259 " --> pdb=" O SER D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 285 removed outlier: 3.503A pdb=" N PHE D 283 " --> pdb=" O ALA D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 312 Processing helix chain 'D' and resid 317 through 332 removed outlier: 3.836A pdb=" N ILE D 321 " --> pdb=" O SER D 317 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 59 through 61 Processing sheet with id=AA2, first strand: chain 'B' and resid 67 through 71 removed outlier: 3.713A pdb=" N MET B 68 " --> pdb=" O TRP B 28 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N CYS B 27 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLN B 38 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY B 34 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 47 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU B 238 " --> pdb=" O THR B 226 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LYS B 240 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N THR B 224 " --> pdb=" O LYS B 240 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 110 through 112 removed outlier: 3.563A pdb=" N VAL B 111 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 205 " --> pdb=" O ILE A 160 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 206 through 207 removed outlier: 4.523A pdb=" N ALA B 157 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER B 172 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL B 167 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE C 88 " --> pdb=" O LEU C 6 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 67 through 71 removed outlier: 3.863A pdb=" N ALA C 26 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLU C 25 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N MET C 40 " --> pdb=" O GLU C 25 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N CYS C 27 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLN C 38 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY C 245 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU C 251 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU C 238 " --> pdb=" O THR C 226 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS C 240 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N THR C 224 " --> pdb=" O LYS C 240 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL C 136 " --> pdb=" O GLU C 198 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU C 198 " --> pdb=" O VAL C 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 124 through 127 removed outlier: 3.753A pdb=" N GLY D 348 " --> pdb=" O GLN C 125 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLY C 127 " --> pdb=" O VAL D 346 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL D 346 " --> pdb=" O GLY C 127 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 204 through 208 removed outlier: 4.863A pdb=" N ALA C 157 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER C 172 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU A 99 " --> pdb=" O MET A 116 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR A 59 " --> pdb=" O ARG A 5 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 67 through 71 removed outlier: 3.620A pdb=" N MET A 68 " --> pdb=" O TRP A 28 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY A 34 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY A 245 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR A 249 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER A 228 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LYS A 240 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N THR A 224 " --> pdb=" O LYS A 240 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 136 " --> pdb=" O GLU A 198 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU A 198 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 18 through 21 removed outlier: 3.571A pdb=" N ARG D 19 " --> pdb=" O GLU D 206 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE D 204 " --> pdb=" O ASN D 21 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 152 through 154 removed outlier: 6.799A pdb=" N LYS D 30 " --> pdb=" O ALA D 174 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ALA D 176 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ALA D 32 " --> pdb=" O ALA D 176 " (cutoff:3.500A) 403 hydrogen bonds defined for protein. 1152 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 3.55 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2732 1.34 - 1.46: 2131 1.46 - 1.58: 4920 1.58 - 1.70: 102 1.70 - 1.82: 102 Bond restraints: 9987 Sorted by residual: bond pdb=" C THR C 219 " pdb=" N PRO C 220 " ideal model delta sigma weight residual 1.335 1.362 -0.027 9.40e-03 1.13e+04 8.22e+00 bond pdb=" CB ASP C 113 " pdb=" CG ASP C 113 " ideal model delta sigma weight residual 1.516 1.570 -0.054 2.50e-02 1.60e+03 4.66e+00 bond pdb=" CB GLU B 132 " pdb=" CG GLU B 132 " ideal model delta sigma weight residual 1.520 1.579 -0.059 3.00e-02 1.11e+03 3.91e+00 bond pdb=" CB ASP A 113 " pdb=" CG ASP A 113 " ideal model delta sigma weight residual 1.516 1.562 -0.046 2.50e-02 1.60e+03 3.38e+00 bond pdb=" CB GLU B 174 " pdb=" CG GLU B 174 " ideal model delta sigma weight residual 1.520 1.566 -0.046 3.00e-02 1.11e+03 2.31e+00 ... (remaining 9982 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 13130 2.27 - 4.53: 441 4.53 - 6.80: 78 6.80 - 9.06: 37 9.06 - 11.33: 10 Bond angle restraints: 13696 Sorted by residual: angle pdb=" CA GLU B 132 " pdb=" CB GLU B 132 " pdb=" CG GLU B 132 " ideal model delta sigma weight residual 114.10 123.74 -9.64 2.00e+00 2.50e-01 2.32e+01 angle pdb=" C ALA A 242 " pdb=" N ASP A 243 " pdb=" CA ASP A 243 " ideal model delta sigma weight residual 121.54 130.43 -8.89 1.91e+00 2.74e-01 2.16e+01 angle pdb=" O GLN A 131 " pdb=" C GLN A 131 " pdb=" N GLU A 132 " ideal model delta sigma weight residual 122.39 128.16 -5.77 1.29e+00 6.01e-01 2.00e+01 angle pdb=" C LYS B 254 " pdb=" N ILE B 255 " pdb=" CA ILE B 255 " ideal model delta sigma weight residual 121.70 129.65 -7.95 1.80e+00 3.09e-01 1.95e+01 angle pdb=" CA GLU A 132 " pdb=" CB GLU A 132 " pdb=" CG GLU A 132 " ideal model delta sigma weight residual 114.10 122.26 -8.16 2.00e+00 2.50e-01 1.66e+01 ... (remaining 13691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 5024 17.60 - 35.19: 688 35.19 - 52.79: 280 52.79 - 70.38: 48 70.38 - 87.98: 13 Dihedral angle restraints: 6053 sinusoidal: 2807 harmonic: 3246 Sorted by residual: dihedral pdb=" CA MET C 199 " pdb=" C MET C 199 " pdb=" N ASN C 200 " pdb=" CA ASN C 200 " ideal model delta harmonic sigma weight residual 180.00 156.09 23.91 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA ASN B 71 " pdb=" C ASN B 71 " pdb=" N LEU B 72 " pdb=" CA LEU B 72 " ideal model delta harmonic sigma weight residual -180.00 -156.78 -23.22 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA ILE D 33 " pdb=" C ILE D 33 " pdb=" N ASP D 34 " pdb=" CA ASP D 34 " ideal model delta harmonic sigma weight residual 180.00 157.56 22.44 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 6050 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1181 0.054 - 0.108: 290 0.108 - 0.162: 80 0.162 - 0.216: 21 0.216 - 0.270: 6 Chirality restraints: 1578 Sorted by residual: chirality pdb=" CA THR A 219 " pdb=" N THR A 219 " pdb=" C THR A 219 " pdb=" CB THR A 219 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CB VAL A 236 " pdb=" CA VAL A 236 " pdb=" CG1 VAL A 236 " pdb=" CG2 VAL A 236 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CB ILE D 44 " pdb=" CA ILE D 44 " pdb=" CG1 ILE D 44 " pdb=" CG2 ILE D 44 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 1575 not shown) Planarity restraints: 1583 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 274 " -0.020 2.00e-02 2.50e+03 2.32e-02 1.35e+01 pdb=" CG TRP D 274 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP D 274 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP D 274 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 274 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 274 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 274 " -0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 274 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 274 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 274 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 132 " 0.015 2.00e-02 2.50e+03 2.99e-02 8.92e+00 pdb=" C GLU A 132 " -0.052 2.00e-02 2.50e+03 pdb=" O GLU A 132 " 0.020 2.00e-02 2.50e+03 pdb=" N TYR A 133 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 5 " -0.236 9.50e-02 1.11e+02 1.07e-01 8.83e+00 pdb=" NE ARG A 5 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG A 5 " -0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG A 5 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG A 5 " -0.001 2.00e-02 2.50e+03 ... (remaining 1580 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1834 2.79 - 3.31: 8023 3.31 - 3.84: 17211 3.84 - 4.37: 19369 4.37 - 4.90: 32874 Nonbonded interactions: 79311 Sorted by model distance: nonbonded pdb=" OE2 GLU A 192 " pdb=" OG SER A 223 " model vdw 2.256 3.040 nonbonded pdb=" O MET D 67 " pdb=" OG1 THR D 71 " model vdw 2.306 3.040 nonbonded pdb=" O THR C 216 " pdb=" OG1 THR C 219 " model vdw 2.352 3.040 nonbonded pdb=" OH TYR C 211 " pdb=" O SER D 25 " model vdw 2.357 3.040 nonbonded pdb=" O ASN B 71 " pdb=" OG SER B 74 " model vdw 2.366 3.040 ... (remaining 79306 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 254) selection = (chain 'C' and resid 1 through 254) } 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 group one per residue 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: 2.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.330 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 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 0.062 9987 Z= 0.325 Angle : 1.042 11.331 13696 Z= 0.537 Chirality : 0.056 0.270 1578 Planarity : 0.007 0.107 1583 Dihedral : 18.972 87.975 3944 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.68 (0.21), residues: 1107 helix: -2.74 (0.20), residues: 307 sheet: -2.02 (0.27), residues: 331 loop : -2.36 (0.23), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.004 TRP D 274 HIS 0.007 0.001 HIS D 63 PHE 0.037 0.003 PHE D 27 TYR 0.022 0.003 TYR B 133 ARG 0.024 0.001 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 1.157 Fit side-chains REVERT: B 87 ILE cc_start: 0.8076 (mp) cc_final: 0.7636 (mt) REVERT: B 184 GLN cc_start: 0.6862 (tm-30) cc_final: 0.6492 (tm-30) REVERT: C 201 GLU cc_start: 0.7192 (pt0) cc_final: 0.6919 (pt0) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1752 time to fit residues: 43.5537 Evaluate side-chains 126 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 HIS ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9987 Z= 0.248 Angle : 0.626 6.270 13696 Z= 0.338 Chirality : 0.045 0.166 1578 Planarity : 0.004 0.036 1583 Dihedral : 19.320 72.526 1802 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.14 % Allowed : 8.57 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.22), residues: 1107 helix: -0.72 (0.27), residues: 304 sheet: -1.77 (0.27), residues: 327 loop : -1.96 (0.24), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 274 HIS 0.009 0.001 HIS D 137 PHE 0.012 0.001 PHE D 126 TYR 0.015 0.002 TYR B 133 ARG 0.008 0.001 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 1.135 Fit side-chains REVERT: B 177 ASN cc_start: 0.7813 (t0) cc_final: 0.7566 (t0) REVERT: B 199 MET cc_start: 0.7420 (tmm) cc_final: 0.6767 (tmm) REVERT: C 1 MET cc_start: 0.7594 (tpp) cc_final: 0.7349 (tpp) REVERT: C 201 GLU cc_start: 0.7279 (pt0) cc_final: 0.7045 (pt0) REVERT: A 68 MET cc_start: 0.7996 (ptp) cc_final: 0.7771 (ptp) REVERT: A 135 CYS cc_start: 0.8085 (p) cc_final: 0.7821 (p) REVERT: D 127 THR cc_start: 0.8885 (p) cc_final: 0.8605 (t) REVERT: D 326 LYS cc_start: 0.8047 (pttm) cc_final: 0.7417 (mmtp) outliers start: 11 outliers final: 8 residues processed: 147 average time/residue: 0.1894 time to fit residues: 41.3033 Evaluate side-chains 130 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain D residue 256 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 0.0980 chunk 32 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 70 optimal weight: 0.3980 chunk 28 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 55 ASN ** D 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9987 Z= 0.197 Angle : 0.569 9.131 13696 Z= 0.301 Chirality : 0.043 0.248 1578 Planarity : 0.003 0.038 1583 Dihedral : 18.861 77.157 1802 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.86 % Allowed : 10.94 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.23), residues: 1107 helix: -0.00 (0.28), residues: 307 sheet: -1.68 (0.26), residues: 349 loop : -1.68 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 274 HIS 0.004 0.001 HIS D 137 PHE 0.008 0.001 PHE D 126 TYR 0.014 0.002 TYR A 250 ARG 0.003 0.000 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 1.093 Fit side-chains REVERT: B 177 ASN cc_start: 0.7806 (t0) cc_final: 0.7576 (t0) REVERT: B 184 GLN cc_start: 0.7087 (pp30) cc_final: 0.6700 (pp30) REVERT: C 1 MET cc_start: 0.7424 (tpp) cc_final: 0.7216 (tpp) REVERT: C 209 LEU cc_start: 0.8756 (mt) cc_final: 0.8527 (mt) REVERT: A 135 CYS cc_start: 0.8134 (p) cc_final: 0.7794 (p) REVERT: D 40 TYR cc_start: 0.7842 (m-10) cc_final: 0.7492 (m-10) REVERT: D 44 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8486 (mp) REVERT: D 127 THR cc_start: 0.8982 (p) cc_final: 0.8684 (t) REVERT: D 326 LYS cc_start: 0.8157 (pttm) cc_final: 0.7482 (mmtp) outliers start: 18 outliers final: 12 residues processed: 136 average time/residue: 0.1869 time to fit residues: 37.8265 Evaluate side-chains 125 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 55 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 GLN C 184 GLN ** D 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 9987 Z= 0.353 Angle : 0.648 9.235 13696 Z= 0.339 Chirality : 0.045 0.237 1578 Planarity : 0.004 0.035 1583 Dihedral : 18.834 71.186 1802 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.10 % Allowed : 12.28 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.24), residues: 1107 helix: 0.11 (0.28), residues: 311 sheet: -2.02 (0.27), residues: 300 loop : -1.49 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP D 274 HIS 0.009 0.001 HIS D 276 PHE 0.013 0.002 PHE D 126 TYR 0.019 0.002 TYR D 26 ARG 0.003 0.001 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 1.129 Fit side-chains REVERT: B 116 MET cc_start: 0.7065 (tpt) cc_final: 0.6861 (tpt) REVERT: B 184 GLN cc_start: 0.7466 (pp30) cc_final: 0.7142 (pp30) REVERT: C 1 MET cc_start: 0.7773 (tpp) cc_final: 0.7459 (tpp) REVERT: A 135 CYS cc_start: 0.8191 (p) cc_final: 0.7912 (p) REVERT: D 40 TYR cc_start: 0.8107 (m-10) cc_final: 0.7716 (m-10) REVERT: D 44 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8440 (mp) REVERT: D 152 TYR cc_start: 0.8652 (p90) cc_final: 0.8312 (p90) REVERT: D 326 LYS cc_start: 0.8368 (pttm) cc_final: 0.7674 (mmtp) outliers start: 30 outliers final: 18 residues processed: 145 average time/residue: 0.2004 time to fit residues: 42.2726 Evaluate side-chains 134 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain D residue 44 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.5980 chunk 62 optimal weight: 8.9990 chunk 1 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 94 optimal weight: 0.4980 chunk 76 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 GLN ** D 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9987 Z= 0.228 Angle : 0.588 9.405 13696 Z= 0.307 Chirality : 0.044 0.227 1578 Planarity : 0.003 0.032 1583 Dihedral : 18.665 73.546 1802 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.68 % Allowed : 14.55 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.24), residues: 1107 helix: 0.55 (0.29), residues: 304 sheet: -1.93 (0.27), residues: 299 loop : -1.42 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 274 HIS 0.004 0.001 HIS D 137 PHE 0.010 0.001 PHE D 126 TYR 0.017 0.002 TYR A 250 ARG 0.003 0.000 ARG D 211 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 1.091 Fit side-chains REVERT: B 177 ASN cc_start: 0.7911 (t0) cc_final: 0.7659 (t0) REVERT: C 1 MET cc_start: 0.7701 (tpp) cc_final: 0.7388 (tpp) REVERT: C 91 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.6261 (mtm110) REVERT: A 135 CYS cc_start: 0.8173 (p) cc_final: 0.7914 (p) REVERT: D 40 TYR cc_start: 0.8019 (m-10) cc_final: 0.7644 (m-10) REVERT: D 44 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8600 (mp) REVERT: D 127 THR cc_start: 0.8930 (p) cc_final: 0.8618 (t) REVERT: D 326 LYS cc_start: 0.8349 (pttm) cc_final: 0.7736 (mmtp) outliers start: 26 outliers final: 17 residues processed: 136 average time/residue: 0.1890 time to fit residues: 38.0862 Evaluate side-chains 131 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 91 ARG Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 256 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 110 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 9 optimal weight: 0.0970 chunk 36 optimal weight: 0.0370 chunk 57 optimal weight: 0.9990 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 GLN ** D 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9987 Z= 0.182 Angle : 0.566 10.371 13696 Z= 0.296 Chirality : 0.043 0.243 1578 Planarity : 0.003 0.028 1583 Dihedral : 18.479 73.850 1802 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.10 % Allowed : 15.07 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.25), residues: 1107 helix: 0.75 (0.30), residues: 307 sheet: -1.83 (0.27), residues: 299 loop : -1.28 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 274 HIS 0.003 0.001 HIS D 63 PHE 0.009 0.001 PHE A 169 TYR 0.015 0.001 TYR A 250 ARG 0.003 0.000 ARG D 211 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 1.170 Fit side-chains REVERT: B 119 MET cc_start: 0.7517 (pmm) cc_final: 0.6272 (pmm) REVERT: B 177 ASN cc_start: 0.7902 (t0) cc_final: 0.7690 (t0) REVERT: C 1 MET cc_start: 0.7540 (tpp) cc_final: 0.7309 (tpp) REVERT: C 91 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.6276 (mtm110) REVERT: A 141 SER cc_start: 0.8291 (p) cc_final: 0.8042 (t) REVERT: D 44 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8584 (mp) REVERT: D 127 THR cc_start: 0.8987 (p) cc_final: 0.8689 (t) REVERT: D 326 LYS cc_start: 0.8406 (pttm) cc_final: 0.7726 (mmtp) outliers start: 30 outliers final: 19 residues processed: 144 average time/residue: 0.1875 time to fit residues: 39.9739 Evaluate side-chains 139 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 91 ARG Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain D residue 44 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 GLN ** D 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9987 Z= 0.276 Angle : 0.610 10.968 13696 Z= 0.317 Chirality : 0.045 0.243 1578 Planarity : 0.003 0.028 1583 Dihedral : 18.503 73.060 1802 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.89 % Allowed : 16.62 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.24), residues: 1107 helix: 0.71 (0.29), residues: 305 sheet: -1.90 (0.27), residues: 294 loop : -1.28 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 274 HIS 0.003 0.001 HIS D 137 PHE 0.010 0.002 PHE D 126 TYR 0.017 0.002 TYR A 250 ARG 0.002 0.000 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 1.026 Fit side-chains REVERT: B 119 MET cc_start: 0.7535 (pmm) cc_final: 0.7284 (pmm) REVERT: B 177 ASN cc_start: 0.7962 (t0) cc_final: 0.7739 (t0) REVERT: B 199 MET cc_start: 0.7415 (tmm) cc_final: 0.7115 (tpp) REVERT: C 1 MET cc_start: 0.7610 (tpp) cc_final: 0.7268 (tpp) REVERT: C 91 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.6270 (mtm110) REVERT: D 44 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8646 (mp) REVERT: D 127 THR cc_start: 0.9035 (p) cc_final: 0.8738 (t) outliers start: 28 outliers final: 23 residues processed: 137 average time/residue: 0.1914 time to fit residues: 38.8056 Evaluate side-chains 135 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 91 ARG Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 256 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 10 optimal weight: 0.0870 chunk 86 optimal weight: 0.0770 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 GLN C 184 GLN D 63 HIS ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9987 Z= 0.179 Angle : 0.573 8.951 13696 Z= 0.301 Chirality : 0.043 0.167 1578 Planarity : 0.003 0.031 1583 Dihedral : 18.390 73.719 1802 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.89 % Allowed : 17.13 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.25), residues: 1107 helix: 0.86 (0.30), residues: 307 sheet: -1.84 (0.27), residues: 304 loop : -1.17 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 274 HIS 0.003 0.001 HIS D 63 PHE 0.009 0.001 PHE C 169 TYR 0.015 0.001 TYR A 250 ARG 0.002 0.000 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 1.005 Fit side-chains REVERT: B 119 MET cc_start: 0.7391 (pmm) cc_final: 0.6473 (pmm) REVERT: B 199 MET cc_start: 0.7372 (tmm) cc_final: 0.7165 (tpt) REVERT: C 91 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.6239 (mtm110) REVERT: C 131 GLN cc_start: 0.7643 (pt0) cc_final: 0.7440 (pt0) REVERT: A 141 SER cc_start: 0.8229 (p) cc_final: 0.8011 (t) REVERT: A 150 ASP cc_start: 0.8149 (m-30) cc_final: 0.7602 (m-30) REVERT: D 44 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8648 (mp) REVERT: D 127 THR cc_start: 0.9056 (p) cc_final: 0.8777 (t) REVERT: D 326 LYS cc_start: 0.8471 (pttt) cc_final: 0.7528 (mmtp) outliers start: 28 outliers final: 23 residues processed: 146 average time/residue: 0.1800 time to fit residues: 38.8370 Evaluate side-chains 143 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 91 ARG Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 270 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.0670 chunk 102 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 80 optimal weight: 0.2980 chunk 31 optimal weight: 0.0050 chunk 92 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 108 optimal weight: 0.0970 chunk 66 optimal weight: 0.7980 overall best weight: 0.2130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 184 GLN ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9987 Z= 0.157 Angle : 0.573 10.586 13696 Z= 0.298 Chirality : 0.043 0.242 1578 Planarity : 0.003 0.029 1583 Dihedral : 18.241 74.659 1802 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.06 % Allowed : 18.78 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.25), residues: 1107 helix: 0.97 (0.30), residues: 311 sheet: -1.56 (0.27), residues: 317 loop : -1.10 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 274 HIS 0.002 0.000 HIS B 246 PHE 0.011 0.001 PHE A 169 TYR 0.012 0.001 TYR A 250 ARG 0.002 0.000 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 1.090 Fit side-chains REVERT: B 119 MET cc_start: 0.7322 (pmm) cc_final: 0.6221 (pmm) REVERT: C 91 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.6225 (mtm110) REVERT: D 44 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8606 (mp) REVERT: D 127 THR cc_start: 0.9053 (p) cc_final: 0.8777 (t) REVERT: D 326 LYS cc_start: 0.8467 (pttt) cc_final: 0.7487 (mmtp) outliers start: 20 outliers final: 13 residues processed: 140 average time/residue: 0.1961 time to fit residues: 40.2170 Evaluate side-chains 137 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 91 ARG Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain D residue 40 TYR Chi-restraints excluded: chain D residue 44 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.2980 chunk 75 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 90 optimal weight: 0.0000 chunk 9 optimal weight: 0.0270 chunk 69 optimal weight: 0.0060 chunk 55 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 chunk 27 optimal weight: 0.4980 overall best weight: 0.1658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 184 GLN ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9987 Z= 0.157 Angle : 0.591 12.658 13696 Z= 0.304 Chirality : 0.043 0.226 1578 Planarity : 0.003 0.028 1583 Dihedral : 18.135 75.058 1802 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.44 % Allowed : 19.71 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.25), residues: 1107 helix: 1.07 (0.30), residues: 312 sheet: -1.48 (0.27), residues: 316 loop : -0.99 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 274 HIS 0.002 0.001 HIS B 246 PHE 0.013 0.001 PHE D 68 TYR 0.018 0.001 TYR A 133 ARG 0.002 0.000 ARG A 5 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 1.005 Fit side-chains REVERT: B 119 MET cc_start: 0.7261 (pmm) cc_final: 0.6965 (pmm) REVERT: C 40 MET cc_start: 0.8272 (ttm) cc_final: 0.7894 (ttm) REVERT: C 91 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.6245 (mtm110) REVERT: A 199 MET cc_start: 0.4878 (mmm) cc_final: 0.4371 (mmm) REVERT: D 44 ILE cc_start: 0.8979 (OUTLIER) cc_final: 0.8614 (mp) REVERT: D 127 THR cc_start: 0.9059 (p) cc_final: 0.8785 (t) REVERT: D 326 LYS cc_start: 0.8471 (pttt) cc_final: 0.7494 (mmtp) outliers start: 14 outliers final: 9 residues processed: 135 average time/residue: 0.2138 time to fit residues: 41.4808 Evaluate side-chains 128 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 91 ARG Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain D residue 44 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.146631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.116215 restraints weight = 14692.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.119604 restraints weight = 10632.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.120457 restraints weight = 7754.513| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9987 Z= 0.274 Angle : 0.638 11.852 13696 Z= 0.326 Chirality : 0.044 0.248 1578 Planarity : 0.003 0.030 1583 Dihedral : 18.238 75.764 1802 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.75 % Allowed : 19.81 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.25), residues: 1107 helix: 0.86 (0.29), residues: 311 sheet: -1.48 (0.27), residues: 325 loop : -1.05 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 274 HIS 0.007 0.001 HIS D 276 PHE 0.018 0.002 PHE D 68 TYR 0.020 0.002 TYR A 133 ARG 0.002 0.000 ARG C 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2041.30 seconds wall clock time: 38 minutes 25.79 seconds (2305.79 seconds total)