Starting phenix.real_space_refine on Wed Jun 11 05:44:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ucs_42139/06_2025/8ucs_42139.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ucs_42139/06_2025/8ucs_42139.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ucs_42139/06_2025/8ucs_42139.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ucs_42139/06_2025/8ucs_42139.map" model { file = "/net/cci-nas-00/data/ceres_data/8ucs_42139/06_2025/8ucs_42139.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ucs_42139/06_2025/8ucs_42139.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.073 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 102 5.16 5 C 8038 2.51 5 N 2087 2.21 5 O 2378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12605 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 362 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 45, 354 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Conformer: "B" Number of residues, atoms: 45, 354 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} bond proxies already assigned to first conformer: 351 Chain: "B" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 394 Classifications: {'peptide': 50} Link IDs: {'TRANS': 49} Chain: "C" Number of atoms: 1942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1942 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 8, 'TRANS': 244} Chain: "D" Number of atoms: 1978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1978 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 8, 'TRANS': 248} Chain: "E" Number of atoms: 1942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1942 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 8, 'TRANS': 244} Chain: "F" Number of atoms: 1978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1978 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 8, 'TRANS': 248} Chain: "G" Number of atoms: 1943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1943 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 8, 'TRANS': 244} Chain: "H" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 688 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "I" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 688 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "J" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 688 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 9.29, per 1000 atoms: 0.74 Number of scatterers: 12605 At special positions: 0 Unit cell: (98.406, 114.345, 127.512, 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 102 16.00 O 2378 8.00 N 2087 7.00 C 8038 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 1.6 seconds 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2996 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 1 sheets defined 86.6% alpha, 0.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 19 through 40 removed outlier: 3.799A pdb=" N PHE A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 60 Processing helix chain 'B' and resid 17 through 40 removed outlier: 4.131A pdb=" N ALA B 21 " --> pdb=" O ASP B 17 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR B 22 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 60 Processing helix chain 'C' and resid 8 through 24 removed outlier: 3.608A pdb=" N VAL C 13 " --> pdb=" O PRO C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.571A pdb=" N VAL C 32 " --> pdb=" O ASN C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 54 Processing helix chain 'C' and resid 57 through 72 removed outlier: 3.799A pdb=" N LYS C 71 " --> pdb=" O ARG C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 95 removed outlier: 3.609A pdb=" N ARG C 93 " --> pdb=" O ARG C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 98 No H-bonds generated for 'chain 'C' and resid 96 through 98' Processing helix chain 'C' and resid 99 through 105 removed outlier: 3.550A pdb=" N ASN C 105 " --> pdb=" O ASP C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 120 Processing helix chain 'C' and resid 123 through 174 Proline residue: C 157 - end of helix Processing helix chain 'C' and resid 177 through 189 removed outlier: 3.671A pdb=" N GLY C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 202 Processing helix chain 'C' and resid 202 through 233 removed outlier: 4.177A pdb=" N GLY C 227 " --> pdb=" O MET C 223 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ALA C 230 " --> pdb=" O GLU C 226 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN C 232 " --> pdb=" O VAL C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 245 Processing helix chain 'C' and resid 249 through 258 Processing helix chain 'D' and resid 6 through 24 Processing helix chain 'D' and resid 29 through 34 Processing helix chain 'D' and resid 35 through 42 Processing helix chain 'D' and resid 42 through 54 Processing helix chain 'D' and resid 55 through 70 removed outlier: 3.608A pdb=" N PHE D 70 " --> pdb=" O ILE D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 95 removed outlier: 3.662A pdb=" N ILE D 81 " --> pdb=" O ASN D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 121 Processing helix chain 'D' and resid 123 through 174 Proline residue: D 157 - end of helix Processing helix chain 'D' and resid 177 through 202 removed outlier: 3.678A pdb=" N THR D 192 " --> pdb=" O ALA D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 233 Processing helix chain 'D' and resid 239 through 245 removed outlier: 3.740A pdb=" N VAL D 245 " --> pdb=" O GLU D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 248 No H-bonds generated for 'chain 'D' and resid 246 through 248' Processing helix chain 'D' and resid 249 through 258 removed outlier: 4.454A pdb=" N GLN D 254 " --> pdb=" O PRO D 250 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ALA D 255 " --> pdb=" O PRO D 251 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS D 258 " --> pdb=" O GLN D 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 24 removed outlier: 3.742A pdb=" N VAL E 13 " --> pdb=" O PRO E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.764A pdb=" N VAL E 32 " --> pdb=" O ASN E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 54 removed outlier: 3.514A pdb=" N PHE E 40 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 70 removed outlier: 3.603A pdb=" N PHE E 70 " --> pdb=" O ILE E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 94 Processing helix chain 'E' and resid 100 through 105 removed outlier: 3.543A pdb=" N ASN E 104 " --> pdb=" O GLU E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 119 Processing helix chain 'E' and resid 123 through 174 Proline residue: E 157 - end of helix removed outlier: 3.521A pdb=" N ASN E 174 " --> pdb=" O GLN E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 189 Processing helix chain 'E' and resid 189 through 202 Processing helix chain 'E' and resid 202 through 234 Processing helix chain 'E' and resid 236 through 246 removed outlier: 3.649A pdb=" N SER E 246 " --> pdb=" O GLU E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 258 Processing helix chain 'F' and resid 6 through 24 Processing helix chain 'F' and resid 29 through 34 Processing helix chain 'F' and resid 35 through 54 removed outlier: 3.618A pdb=" N GLY F 44 " --> pdb=" O PHE F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 70 Processing helix chain 'F' and resid 76 through 95 Processing helix chain 'F' and resid 96 through 98 No H-bonds generated for 'chain 'F' and resid 96 through 98' Processing helix chain 'F' and resid 99 through 105 removed outlier: 3.548A pdb=" N ASN F 105 " --> pdb=" O ASP F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 121 Processing helix chain 'F' and resid 123 through 174 Proline residue: F 157 - end of helix removed outlier: 3.580A pdb=" N ASN F 174 " --> pdb=" O GLN F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 202 removed outlier: 3.654A pdb=" N THR F 192 " --> pdb=" O ALA F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 234 Processing helix chain 'F' and resid 238 through 245 removed outlier: 3.611A pdb=" N GLU F 242 " --> pdb=" O ARG F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 248 No H-bonds generated for 'chain 'F' and resid 246 through 248' Processing helix chain 'F' and resid 249 through 254 removed outlier: 4.193A pdb=" N GLN F 254 " --> pdb=" O PRO F 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 26 removed outlier: 3.745A pdb=" N GLY G 26 " --> pdb=" O GLY G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 35 through 54 Processing helix chain 'G' and resid 55 through 72 removed outlier: 3.581A pdb=" N PHE G 70 " --> pdb=" O ILE G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 94 Processing helix chain 'G' and resid 95 through 98 removed outlier: 3.589A pdb=" N SER G 98 " --> pdb=" O GLY G 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 95 through 98' Processing helix chain 'G' and resid 99 through 105 Processing helix chain 'G' and resid 111 through 120 removed outlier: 3.643A pdb=" N VAL G 118 " --> pdb=" O GLY G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 174 Proline residue: G 157 - end of helix Processing helix chain 'G' and resid 177 through 179 No H-bonds generated for 'chain 'G' and resid 177 through 179' Processing helix chain 'G' and resid 180 through 189 Processing helix chain 'G' and resid 189 through 202 Processing helix chain 'G' and resid 202 through 233 Processing helix chain 'G' and resid 236 through 246 removed outlier: 3.884A pdb=" N SER G 246 " --> pdb=" O GLU G 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 249 through 260 removed outlier: 3.520A pdb=" N GLN G 254 " --> pdb=" O PRO G 250 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL G 259 " --> pdb=" O ALA G 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 255 Processing helix chain 'H' and resid 259 through 266 removed outlier: 3.531A pdb=" N ALA H 264 " --> pdb=" O THR H 260 " (cutoff:3.500A) Processing helix chain 'H' and resid 271 through 280 Processing helix chain 'H' and resid 283 through 295 Processing helix chain 'H' and resid 304 through 320 Processing helix chain 'I' and resid 239 through 244 removed outlier: 4.130A pdb=" N ILE I 244 " --> pdb=" O GLU I 241 " (cutoff:3.500A) Processing helix chain 'I' and resid 247 through 256 removed outlier: 3.539A pdb=" N ARG I 253 " --> pdb=" O VAL I 249 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL I 254 " --> pdb=" O ALA I 250 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG I 256 " --> pdb=" O GLN I 252 " (cutoff:3.500A) Processing helix chain 'I' and resid 259 through 268 removed outlier: 3.835A pdb=" N LYS I 268 " --> pdb=" O ALA I 264 " (cutoff:3.500A) Processing helix chain 'I' and resid 271 through 281 removed outlier: 3.665A pdb=" N ALA I 275 " --> pdb=" O SER I 271 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL I 277 " --> pdb=" O GLU I 273 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN I 281 " --> pdb=" O VAL I 277 " (cutoff:3.500A) Processing helix chain 'I' and resid 283 through 296 Processing helix chain 'I' and resid 301 through 319 removed outlier: 3.573A pdb=" N GLN I 310 " --> pdb=" O GLU I 306 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY I 311 " --> pdb=" O LYS I 307 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE I 316 " --> pdb=" O ILE I 312 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG I 317 " --> pdb=" O VAL I 313 " (cutoff:3.500A) Processing helix chain 'J' and resid 247 through 256 removed outlier: 3.787A pdb=" N GLN J 252 " --> pdb=" O ASP J 248 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG J 253 " --> pdb=" O VAL J 249 " (cutoff:3.500A) Processing helix chain 'J' and resid 259 through 268 removed outlier: 3.562A pdb=" N LYS J 268 " --> pdb=" O ALA J 264 " (cutoff:3.500A) Processing helix chain 'J' and resid 271 through 279 Processing helix chain 'J' and resid 283 through 298 removed outlier: 3.733A pdb=" N SER J 288 " --> pdb=" O LYS J 284 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU J 292 " --> pdb=" O SER J 288 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU J 295 " --> pdb=" O LYS J 291 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLY J 298 " --> pdb=" O ILE J 294 " (cutoff:3.500A) Processing helix chain 'J' and resid 302 through 319 removed outlier: 4.138A pdb=" N GLU J 306 " --> pdb=" O ILE J 302 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS J 307 " --> pdb=" O MET J 303 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE J 316 " --> pdb=" O ILE J 312 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 43 991 hydrogen bonds defined for protein. 2928 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.87 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4116 1.34 - 1.46: 2682 1.46 - 1.58: 5786 1.58 - 1.70: 0 1.70 - 1.81: 199 Bond restraints: 12783 Sorted by residual: bond pdb=" CB GLU I 292 " pdb=" CG GLU I 292 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.14e+00 bond pdb=" CB ASP J 293 " pdb=" CG ASP J 293 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 9.72e-01 bond pdb=" CB MET H 303 " pdb=" CG MET H 303 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.62e-01 bond pdb=" CB ASP F 86 " pdb=" CG ASP F 86 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.39e-01 bond pdb=" CB ASP I 262 " pdb=" CG ASP I 262 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.26e-01 ... (remaining 12778 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 17026 1.81 - 3.63: 147 3.63 - 5.44: 43 5.44 - 7.25: 6 7.25 - 9.06: 3 Bond angle restraints: 17225 Sorted by residual: angle pdb=" CA MET H 303 " pdb=" CB MET H 303 " pdb=" CG MET H 303 " ideal model delta sigma weight residual 114.10 121.90 -7.80 2.00e+00 2.50e-01 1.52e+01 angle pdb=" CB MET H 303 " pdb=" CG MET H 303 " pdb=" SD MET H 303 " ideal model delta sigma weight residual 112.70 121.76 -9.06 3.00e+00 1.11e-01 9.13e+00 angle pdb=" N ILE F 6 " pdb=" CA ILE F 6 " pdb=" C ILE F 6 " ideal model delta sigma weight residual 113.10 110.36 2.74 9.70e-01 1.06e+00 7.98e+00 angle pdb=" CA GLU J 273 " pdb=" CB GLU J 273 " pdb=" CG GLU J 273 " ideal model delta sigma weight residual 114.10 119.62 -5.52 2.00e+00 2.50e-01 7.62e+00 angle pdb=" C ASP E 108 " pdb=" N ASP E 109 " pdb=" CA ASP E 109 " ideal model delta sigma weight residual 121.54 126.71 -5.17 1.91e+00 2.74e-01 7.33e+00 ... (remaining 17220 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 6588 17.83 - 35.66: 852 35.66 - 53.48: 260 53.48 - 71.31: 55 71.31 - 89.14: 19 Dihedral angle restraints: 7774 sinusoidal: 3122 harmonic: 4652 Sorted by residual: dihedral pdb=" CA GLY C 227 " pdb=" C GLY C 227 " pdb=" N VAL C 228 " pdb=" CA VAL C 228 " ideal model delta harmonic sigma weight residual 180.00 161.09 18.91 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA VAL D 202 " pdb=" C VAL D 202 " pdb=" N PHE D 203 " pdb=" CA PHE D 203 " ideal model delta harmonic sigma weight residual -180.00 -161.48 -18.52 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA VAL F 202 " pdb=" C VAL F 202 " pdb=" N PHE F 203 " pdb=" CA PHE F 203 " ideal model delta harmonic sigma weight residual -180.00 -161.56 -18.44 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 7771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1473 0.037 - 0.074: 450 0.074 - 0.111: 81 0.111 - 0.148: 7 0.148 - 0.185: 1 Chirality restraints: 2012 Sorted by residual: chirality pdb=" CA THR F 8 " pdb=" N THR F 8 " pdb=" C THR F 8 " pdb=" CB THR F 8 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.56e-01 chirality pdb=" CG LEU E 172 " pdb=" CB LEU E 172 " pdb=" CD1 LEU E 172 " pdb=" CD2 LEU E 172 " both_signs ideal model delta sigma weight residual False -2.59 -2.72 0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA ILE C 122 " pdb=" N ILE C 122 " pdb=" C ILE C 122 " pdb=" CB ILE C 122 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 ... (remaining 2009 not shown) Planarity restraints: 2184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET H 303 " 0.012 2.00e-02 2.50e+03 2.30e-02 5.28e+00 pdb=" C MET H 303 " -0.040 2.00e-02 2.50e+03 pdb=" O MET H 303 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP H 304 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN E 236 " -0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO E 237 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO E 237 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 237 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 250 " 0.028 5.00e-02 4.00e+02 4.15e-02 2.76e+00 pdb=" N PRO C 251 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 251 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 251 " 0.024 5.00e-02 4.00e+02 ... (remaining 2181 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2490 2.77 - 3.30: 12723 3.30 - 3.83: 22411 3.83 - 4.37: 26233 4.37 - 4.90: 43397 Nonbonded interactions: 107254 Sorted by model distance: nonbonded pdb=" NH2 ARG C 238 " pdb=" OD2 ASP D 120 " model vdw 2.235 3.120 nonbonded pdb=" O GLY G 95 " pdb=" OG SER G 98 " model vdw 2.260 3.040 nonbonded pdb=" O GLY F 95 " pdb=" OG SER F 98 " model vdw 2.271 3.040 nonbonded pdb=" O ARG H 253 " pdb=" NH1 ARG H 253 " model vdw 2.274 3.120 nonbonded pdb=" O GLY D 22 " pdb=" OG SER D 25 " model vdw 2.281 3.040 ... (remaining 107249 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' and (resid 16 through 32 or resid 34 through 60)) selection = (chain 'B' and (resid 16 through 32 or resid 34 through 60)) } ncs_group { reference = (chain 'C' and resid 8 through 259) selection = (chain 'D' and resid 8 through 259) selection = (chain 'E' and resid 8 through 259) selection = (chain 'F' and resid 8 through 259) selection = (chain 'G' and resid 8 through 259) } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.37 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: 3.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.260 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:12.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12783 Z= 0.105 Angle : 0.485 9.064 17225 Z= 0.253 Chirality : 0.036 0.185 2012 Planarity : 0.004 0.051 2184 Dihedral : 18.156 89.141 4778 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.36 % Allowed : 28.89 % Favored : 70.74 % 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: 0.55 (0.20), residues: 1613 helix: 0.70 (0.14), residues: 1354 sheet: None (None), residues: 0 loop : -0.95 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 21 HIS 0.001 0.000 HIS D 142 PHE 0.016 0.001 PHE C 59 TYR 0.006 0.001 TYR F 256 ARG 0.005 0.000 ARG I 317 Details of bonding type rmsd hydrogen bonds : bond 0.21686 ( 991) hydrogen bonds : angle 7.31428 ( 2928) covalent geometry : bond 0.00252 (12783) covalent geometry : angle 0.48520 (17225) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 250 time to evaluate : 1.463 Fit side-chains revert: symmetry clash REVERT: D 223 MET cc_start: 0.8604 (ptm) cc_final: 0.8391 (ptt) REVERT: F 104 ASN cc_start: 0.7700 (m-40) cc_final: 0.7267 (m110) REVERT: F 108 ASP cc_start: 0.7627 (t70) cc_final: 0.7171 (t70) outliers start: 4 outliers final: 4 residues processed: 253 average time/residue: 1.3722 time to fit residues: 374.3584 Evaluate side-chains 237 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 233 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain F residue 14 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 0.9980 chunk 119 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN C 29 ASN D 29 ASN F 254 GLN J 252 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.198374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.128597 restraints weight = 12623.283| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.98 r_work: 0.3165 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12783 Z= 0.154 Angle : 0.553 7.793 17225 Z= 0.301 Chirality : 0.040 0.167 2012 Planarity : 0.005 0.049 2184 Dihedral : 4.836 52.581 1743 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.73 % Allowed : 24.75 % Favored : 70.52 % 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 (0.21), residues: 1613 helix: 1.44 (0.14), residues: 1379 sheet: None (None), residues: 0 loop : -0.98 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 19 HIS 0.001 0.001 HIS G 142 PHE 0.022 0.002 PHE B 48 TYR 0.009 0.001 TYR F 110 ARG 0.004 0.000 ARG C 238 Details of bonding type rmsd hydrogen bonds : bond 0.05199 ( 991) hydrogen bonds : angle 4.54020 ( 2928) covalent geometry : bond 0.00334 (12783) covalent geometry : angle 0.55328 (17225) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 258 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 47 LYS cc_start: 0.7693 (tmtt) cc_final: 0.6979 (mttm) REVERT: B 56 GLN cc_start: 0.7389 (mt0) cc_final: 0.7176 (mm-40) REVERT: C 68 GLN cc_start: 0.7048 (tm-30) cc_final: 0.6536 (tm-30) REVERT: C 72 ASP cc_start: 0.5659 (OUTLIER) cc_final: 0.4906 (p0) REVERT: C 187 LYS cc_start: 0.8398 (mppt) cc_final: 0.7541 (mmtm) REVERT: D 35 ASP cc_start: 0.9105 (t70) cc_final: 0.8884 (t70) REVERT: D 223 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8590 (ttt) REVERT: D 243 LYS cc_start: 0.6672 (ptpt) cc_final: 0.6452 (pttt) REVERT: F 14 LEU cc_start: 0.8355 (mt) cc_final: 0.8003 (tp) REVERT: F 108 ASP cc_start: 0.7506 (t70) cc_final: 0.7070 (t70) REVERT: F 129 GLU cc_start: 0.7502 (tm-30) cc_final: 0.7263 (pt0) REVERT: G 56 MET cc_start: 0.7604 (tpt) cc_final: 0.7377 (mmp) REVERT: G 141 ARG cc_start: 0.8118 (mtm-85) cc_final: 0.7724 (mtm110) outliers start: 64 outliers final: 19 residues processed: 293 average time/residue: 1.3270 time to fit residues: 419.9071 Evaluate side-chains 262 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 241 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain D residue 223 MET Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain I residue 318 ARG Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 249 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 108 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 137 optimal weight: 8.9990 chunk 51 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 0.0010 chunk 8 optimal weight: 1.9990 chunk 135 optimal weight: 6.9990 chunk 150 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN C 105 ASN D 29 ASN F 254 GLN G 68 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.199042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.131975 restraints weight = 15895.998| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.45 r_work: 0.3204 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12783 Z= 0.135 Angle : 0.515 7.412 17225 Z= 0.279 Chirality : 0.039 0.156 2012 Planarity : 0.005 0.047 2184 Dihedral : 4.456 51.855 1737 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.93 % Allowed : 25.47 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.21), residues: 1613 helix: 1.70 (0.14), residues: 1380 sheet: None (None), residues: 0 loop : -1.07 (0.41), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 19 HIS 0.001 0.000 HIS G 142 PHE 0.021 0.002 PHE B 48 TYR 0.009 0.001 TYR E 110 ARG 0.004 0.000 ARG C 61 Details of bonding type rmsd hydrogen bonds : bond 0.04602 ( 991) hydrogen bonds : angle 4.25605 ( 2928) covalent geometry : bond 0.00289 (12783) covalent geometry : angle 0.51463 (17225) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 243 time to evaluate : 1.481 Fit side-chains revert: symmetry clash REVERT: A 49 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7623 (tp40) REVERT: B 47 LYS cc_start: 0.7707 (tmtt) cc_final: 0.7057 (mttm) REVERT: B 56 GLN cc_start: 0.7482 (mt0) cc_final: 0.7234 (mm-40) REVERT: C 68 GLN cc_start: 0.7054 (tm-30) cc_final: 0.6574 (tm-30) REVERT: C 72 ASP cc_start: 0.5446 (OUTLIER) cc_final: 0.4689 (p0) REVERT: C 187 LYS cc_start: 0.8450 (mppt) cc_final: 0.7611 (mmtm) REVERT: D 185 MET cc_start: 0.8902 (tpt) cc_final: 0.8701 (tpt) REVERT: F 14 LEU cc_start: 0.8445 (mt) cc_final: 0.8134 (tp) REVERT: G 129 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6668 (mp0) REVERT: G 141 ARG cc_start: 0.8053 (mtm-85) cc_final: 0.7745 (mtm110) REVERT: J 303 MET cc_start: 0.6316 (ttt) cc_final: 0.6056 (mpt) outliers start: 53 outliers final: 22 residues processed: 278 average time/residue: 1.3407 time to fit residues: 401.4839 Evaluate side-chains 258 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 233 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 171 MET Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain J residue 249 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 122 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 70 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 152 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN C 105 ASN D 29 ASN F 254 GLN G 68 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.198154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.133911 restraints weight = 10741.826| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.85 r_work: 0.3181 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12783 Z= 0.139 Angle : 0.516 7.748 17225 Z= 0.279 Chirality : 0.039 0.163 2012 Planarity : 0.005 0.049 2184 Dihedral : 4.491 53.748 1737 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.37 % Allowed : 24.96 % Favored : 70.67 % 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: 2.02 (0.21), residues: 1613 helix: 1.74 (0.14), residues: 1385 sheet: None (None), residues: 0 loop : -1.06 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 19 HIS 0.001 0.001 HIS G 142 PHE 0.022 0.002 PHE B 48 TYR 0.009 0.001 TYR F 110 ARG 0.004 0.000 ARG C 61 Details of bonding type rmsd hydrogen bonds : bond 0.04507 ( 991) hydrogen bonds : angle 4.19352 ( 2928) covalent geometry : bond 0.00304 (12783) covalent geometry : angle 0.51597 (17225) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 243 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7535 (tp40) REVERT: B 47 LYS cc_start: 0.7623 (tmtt) cc_final: 0.6931 (mttm) REVERT: B 56 GLN cc_start: 0.7377 (mm-40) cc_final: 0.7092 (mm-40) REVERT: C 68 GLN cc_start: 0.6954 (tm-30) cc_final: 0.6487 (tm-30) REVERT: C 72 ASP cc_start: 0.5339 (OUTLIER) cc_final: 0.4600 (p0) REVERT: C 187 LYS cc_start: 0.8432 (mppt) cc_final: 0.7503 (mmtm) REVERT: D 35 ASP cc_start: 0.9130 (t70) cc_final: 0.8895 (t70) REVERT: F 14 LEU cc_start: 0.8333 (mt) cc_final: 0.7985 (tp) REVERT: F 108 ASP cc_start: 0.7550 (t70) cc_final: 0.7094 (t70) REVERT: G 129 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.6611 (mp0) REVERT: G 141 ARG cc_start: 0.8047 (mtm-85) cc_final: 0.7682 (mtm110) REVERT: J 303 MET cc_start: 0.6372 (ttt) cc_final: 0.6085 (mpt) outliers start: 59 outliers final: 29 residues processed: 282 average time/residue: 1.5796 time to fit residues: 478.9777 Evaluate side-chains 267 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 235 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 171 MET Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain I residue 318 ARG Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 249 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 115 optimal weight: 5.9990 chunk 104 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 138 optimal weight: 0.3980 chunk 91 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN C 105 ASN C 200 ASN D 29 ASN ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN ** J 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.197968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.127776 restraints weight = 12491.215| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.93 r_work: 0.3185 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12783 Z= 0.141 Angle : 0.518 8.026 17225 Z= 0.279 Chirality : 0.039 0.164 2012 Planarity : 0.005 0.050 2184 Dihedral : 4.503 54.968 1737 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.66 % Allowed : 24.96 % Favored : 70.38 % 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: 2.07 (0.21), residues: 1613 helix: 1.77 (0.14), residues: 1387 sheet: None (None), residues: 0 loop : -0.99 (0.41), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 19 HIS 0.001 0.001 HIS G 142 PHE 0.023 0.002 PHE B 48 TYR 0.009 0.001 TYR F 110 ARG 0.005 0.000 ARG C 61 Details of bonding type rmsd hydrogen bonds : bond 0.04481 ( 991) hydrogen bonds : angle 4.16102 ( 2928) covalent geometry : bond 0.00308 (12783) covalent geometry : angle 0.51809 (17225) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 238 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7565 (tp40) REVERT: B 47 LYS cc_start: 0.7721 (tmtt) cc_final: 0.7056 (mttm) REVERT: B 55 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7709 (ttm) REVERT: B 56 GLN cc_start: 0.7414 (mm-40) cc_final: 0.7118 (mm-40) REVERT: C 68 GLN cc_start: 0.6952 (tm-30) cc_final: 0.6516 (tm-30) REVERT: C 72 ASP cc_start: 0.5356 (OUTLIER) cc_final: 0.4612 (p0) REVERT: C 187 LYS cc_start: 0.8419 (mppt) cc_final: 0.7532 (mmtm) REVERT: D 35 ASP cc_start: 0.9124 (t70) cc_final: 0.8884 (t70) REVERT: F 14 LEU cc_start: 0.8369 (mt) cc_final: 0.8030 (tp) REVERT: F 59 PHE cc_start: 0.8462 (t80) cc_final: 0.8257 (t80) REVERT: F 108 ASP cc_start: 0.7583 (t70) cc_final: 0.7121 (t70) REVERT: G 141 ARG cc_start: 0.8085 (mtm-85) cc_final: 0.7727 (mtm110) REVERT: J 303 MET cc_start: 0.6417 (ttt) cc_final: 0.6083 (mpt) outliers start: 63 outliers final: 34 residues processed: 280 average time/residue: 1.4609 time to fit residues: 440.3436 Evaluate side-chains 276 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 239 time to evaluate : 2.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 171 MET Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 232 GLN Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain I residue 318 ARG Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 249 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 34 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 98 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN C 105 ASN D 29 ASN F 254 GLN G 68 GLN ** J 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.198641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.130555 restraints weight = 12724.478| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.04 r_work: 0.3174 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12783 Z= 0.133 Angle : 0.509 7.766 17225 Z= 0.274 Chirality : 0.039 0.163 2012 Planarity : 0.004 0.050 2184 Dihedral : 4.463 54.450 1737 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.15 % Allowed : 25.33 % Favored : 70.52 % 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: 2.18 (0.21), residues: 1613 helix: 1.84 (0.14), residues: 1387 sheet: None (None), residues: 0 loop : -0.99 (0.42), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 19 HIS 0.001 0.001 HIS G 142 PHE 0.021 0.002 PHE B 48 TYR 0.009 0.001 TYR F 110 ARG 0.005 0.000 ARG C 238 Details of bonding type rmsd hydrogen bonds : bond 0.04309 ( 991) hydrogen bonds : angle 4.09485 ( 2928) covalent geometry : bond 0.00289 (12783) covalent geometry : angle 0.50901 (17225) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 243 time to evaluate : 1.346 Fit side-chains revert: symmetry clash REVERT: A 49 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7530 (tp40) REVERT: B 55 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7714 (ttm) REVERT: B 56 GLN cc_start: 0.7396 (mm-40) cc_final: 0.7080 (mm-40) REVERT: C 61 ARG cc_start: 0.7356 (ttp80) cc_final: 0.7054 (ttt180) REVERT: C 68 GLN cc_start: 0.6875 (tm-30) cc_final: 0.6434 (tm-30) REVERT: C 72 ASP cc_start: 0.5254 (OUTLIER) cc_final: 0.4514 (p0) REVERT: C 92 ARG cc_start: 0.7714 (mtp85) cc_final: 0.7322 (mtt-85) REVERT: C 187 LYS cc_start: 0.8447 (mppt) cc_final: 0.7540 (mmtm) REVERT: D 35 ASP cc_start: 0.9138 (t70) cc_final: 0.8903 (t70) REVERT: F 14 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7977 (tp) REVERT: F 108 ASP cc_start: 0.7562 (t70) cc_final: 0.7113 (t70) REVERT: F 129 GLU cc_start: 0.7495 (tm-30) cc_final: 0.7292 (pt0) REVERT: G 141 ARG cc_start: 0.8064 (mtm-85) cc_final: 0.7712 (mtm110) REVERT: J 303 MET cc_start: 0.6422 (ttt) cc_final: 0.6090 (mpt) outliers start: 56 outliers final: 34 residues processed: 279 average time/residue: 1.3334 time to fit residues: 401.5766 Evaluate side-chains 268 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 230 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 171 MET Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain I residue 243 ILE Chi-restraints excluded: chain I residue 316 ILE Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 249 VAL Chi-restraints excluded: chain J residue 271 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 42 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 157 optimal weight: 4.9990 chunk 65 optimal weight: 0.0570 chunk 128 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 61 optimal weight: 0.0870 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN C 105 ASN D 29 ASN ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.200089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.132113 restraints weight = 12569.636| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.02 r_work: 0.3194 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3019 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12783 Z= 0.120 Angle : 0.509 12.698 17225 Z= 0.271 Chirality : 0.038 0.160 2012 Planarity : 0.004 0.051 2184 Dihedral : 4.361 51.949 1737 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.22 % Allowed : 25.47 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.21), residues: 1613 helix: 1.94 (0.14), residues: 1386 sheet: None (None), residues: 0 loop : -0.93 (0.42), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 21 HIS 0.001 0.000 HIS G 142 PHE 0.020 0.002 PHE B 48 TYR 0.009 0.001 TYR F 110 ARG 0.004 0.000 ARG C 61 Details of bonding type rmsd hydrogen bonds : bond 0.04000 ( 991) hydrogen bonds : angle 3.99315 ( 2928) covalent geometry : bond 0.00254 (12783) covalent geometry : angle 0.50926 (17225) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 252 time to evaluate : 1.269 Fit side-chains revert: symmetry clash REVERT: A 49 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7567 (tp40) REVERT: B 47 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.6964 (mttm) REVERT: B 55 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7702 (ttm) REVERT: B 56 GLN cc_start: 0.7411 (mm-40) cc_final: 0.7155 (mm-40) REVERT: C 61 ARG cc_start: 0.7299 (ttp80) cc_final: 0.7065 (ttt180) REVERT: C 68 GLN cc_start: 0.6877 (tm-30) cc_final: 0.6489 (tm-30) REVERT: C 92 ARG cc_start: 0.7710 (mtp85) cc_final: 0.7303 (mtt-85) REVERT: C 187 LYS cc_start: 0.8448 (mppt) cc_final: 0.7541 (mmtm) REVERT: C 249 SER cc_start: 0.8045 (OUTLIER) cc_final: 0.7834 (m) REVERT: D 35 ASP cc_start: 0.9130 (t70) cc_final: 0.8919 (t70) REVERT: F 14 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7958 (tp) REVERT: G 141 ARG cc_start: 0.8081 (mtm-85) cc_final: 0.7703 (mtm110) REVERT: H 303 MET cc_start: 0.5857 (tmm) cc_final: 0.5446 (tmm) REVERT: J 303 MET cc_start: 0.6431 (ttt) cc_final: 0.6100 (mpt) outliers start: 57 outliers final: 28 residues processed: 287 average time/residue: 1.2738 time to fit residues: 395.3237 Evaluate side-chains 277 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 244 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 171 MET Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain I residue 243 ILE Chi-restraints excluded: chain I residue 316 ILE Chi-restraints excluded: chain J residue 249 VAL Chi-restraints excluded: chain J residue 271 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 116 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 44 optimal weight: 0.0270 chunk 86 optimal weight: 0.5980 chunk 146 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 138 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN C 105 ASN D 29 ASN D 83 ASN ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN ** J 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.198939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.131439 restraints weight = 11245.647| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.89 r_work: 0.3206 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12783 Z= 0.133 Angle : 0.526 11.543 17225 Z= 0.280 Chirality : 0.038 0.165 2012 Planarity : 0.005 0.056 2184 Dihedral : 4.434 53.664 1737 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.78 % Allowed : 25.84 % Favored : 70.38 % 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: 2.27 (0.21), residues: 1613 helix: 1.91 (0.14), residues: 1385 sheet: None (None), residues: 0 loop : -0.98 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 21 HIS 0.001 0.000 HIS G 142 PHE 0.023 0.002 PHE F 70 TYR 0.010 0.001 TYR F 110 ARG 0.006 0.000 ARG C 238 Details of bonding type rmsd hydrogen bonds : bond 0.04229 ( 991) hydrogen bonds : angle 4.05919 ( 2928) covalent geometry : bond 0.00292 (12783) covalent geometry : angle 0.52566 (17225) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 240 time to evaluate : 1.321 Fit side-chains revert: symmetry clash REVERT: A 49 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7520 (tp40) REVERT: B 47 LYS cc_start: 0.7626 (OUTLIER) cc_final: 0.6993 (mttm) REVERT: B 56 GLN cc_start: 0.7411 (mm-40) cc_final: 0.7157 (mm-40) REVERT: C 61 ARG cc_start: 0.7319 (ttp80) cc_final: 0.7021 (ttt180) REVERT: C 68 GLN cc_start: 0.6918 (tm-30) cc_final: 0.6492 (tm-30) REVERT: C 72 ASP cc_start: 0.5241 (OUTLIER) cc_final: 0.4515 (p0) REVERT: C 92 ARG cc_start: 0.7752 (mtp85) cc_final: 0.7353 (mtt-85) REVERT: C 187 LYS cc_start: 0.8456 (mppt) cc_final: 0.7556 (mmtm) REVERT: D 35 ASP cc_start: 0.9127 (t70) cc_final: 0.8893 (t70) REVERT: D 123 GLU cc_start: 0.7402 (pm20) cc_final: 0.6884 (tp30) REVERT: F 14 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7990 (tp) REVERT: F 108 ASP cc_start: 0.7586 (t70) cc_final: 0.7115 (t70) REVERT: F 125 GLU cc_start: 0.7340 (pm20) cc_final: 0.6998 (pm20) REVERT: G 141 ARG cc_start: 0.8039 (mtm-85) cc_final: 0.7683 (mtm110) REVERT: H 303 MET cc_start: 0.5874 (tmm) cc_final: 0.5420 (tmm) REVERT: J 303 MET cc_start: 0.6427 (ttt) cc_final: 0.6102 (mpt) outliers start: 51 outliers final: 31 residues processed: 274 average time/residue: 1.2983 time to fit residues: 384.4619 Evaluate side-chains 271 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 236 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 171 MET Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain I residue 243 ILE Chi-restraints excluded: chain I residue 316 ILE Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 249 VAL Chi-restraints excluded: chain J residue 271 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 97 optimal weight: 0.0670 chunk 107 optimal weight: 0.4980 chunk 79 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 11 optimal weight: 0.0980 chunk 114 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN C 105 ASN D 29 ASN D 83 ASN D 174 ASN ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN ** J 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.200728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.132541 restraints weight = 12804.071| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.91 r_work: 0.3234 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3075 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3075 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12783 Z= 0.117 Angle : 0.506 10.793 17225 Z= 0.270 Chirality : 0.038 0.160 2012 Planarity : 0.004 0.056 2184 Dihedral : 4.346 51.164 1737 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.20 % Allowed : 26.35 % Favored : 70.45 % 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: 2.42 (0.22), residues: 1613 helix: 2.01 (0.14), residues: 1386 sheet: None (None), residues: 0 loop : -0.94 (0.42), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 21 HIS 0.001 0.000 HIS G 142 PHE 0.019 0.002 PHE B 48 TYR 0.009 0.001 TYR F 110 ARG 0.013 0.000 ARG D 61 Details of bonding type rmsd hydrogen bonds : bond 0.03876 ( 991) hydrogen bonds : angle 3.95513 ( 2928) covalent geometry : bond 0.00248 (12783) covalent geometry : angle 0.50636 (17225) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 250 time to evaluate : 1.468 Fit side-chains revert: symmetry clash REVERT: A 49 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7491 (tp40) REVERT: B 47 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.6910 (mttm) REVERT: B 55 MET cc_start: 0.7948 (mtp) cc_final: 0.7683 (mtt) REVERT: B 56 GLN cc_start: 0.7392 (mm-40) cc_final: 0.6986 (tp40) REVERT: C 61 ARG cc_start: 0.7299 (ttp80) cc_final: 0.7077 (ttt180) REVERT: C 68 GLN cc_start: 0.6875 (tm-30) cc_final: 0.6448 (tm-30) REVERT: C 72 ASP cc_start: 0.5198 (OUTLIER) cc_final: 0.4515 (p0) REVERT: C 92 ARG cc_start: 0.7719 (mtp85) cc_final: 0.7311 (mtt-85) REVERT: C 187 LYS cc_start: 0.8437 (mppt) cc_final: 0.7527 (mmtm) REVERT: D 123 GLU cc_start: 0.7320 (pm20) cc_final: 0.6804 (tp30) REVERT: F 14 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7959 (tp) REVERT: F 108 ASP cc_start: 0.7558 (t70) cc_final: 0.7103 (t70) REVERT: F 125 GLU cc_start: 0.7302 (pm20) cc_final: 0.6940 (pm20) REVERT: G 141 ARG cc_start: 0.8014 (mtm-85) cc_final: 0.7652 (mtm110) REVERT: H 303 MET cc_start: 0.5825 (tmm) cc_final: 0.5416 (tmm) REVERT: J 303 MET cc_start: 0.6428 (ttt) cc_final: 0.6108 (mpt) outliers start: 43 outliers final: 26 residues processed: 278 average time/residue: 1.4541 time to fit residues: 436.9095 Evaluate side-chains 269 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 239 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 171 MET Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain I residue 243 ILE Chi-restraints excluded: chain I residue 268 LYS Chi-restraints excluded: chain I residue 316 ILE Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 249 VAL Chi-restraints excluded: chain J residue 271 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 120 optimal weight: 0.0070 chunk 136 optimal weight: 7.9990 chunk 142 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN C 105 ASN D 29 ASN D 83 ASN D 174 ASN ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN ** J 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.198055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.132898 restraints weight = 10740.964| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.84 r_work: 0.3186 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12783 Z= 0.148 Angle : 0.546 10.628 17225 Z= 0.291 Chirality : 0.039 0.169 2012 Planarity : 0.005 0.058 2184 Dihedral : 4.500 55.627 1737 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.98 % Allowed : 26.86 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.21), residues: 1613 helix: 1.87 (0.14), residues: 1389 sheet: None (None), residues: 0 loop : -0.89 (0.43), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 21 HIS 0.001 0.001 HIS G 142 PHE 0.023 0.002 PHE C 59 TYR 0.010 0.001 TYR F 110 ARG 0.009 0.000 ARG D 61 Details of bonding type rmsd hydrogen bonds : bond 0.04434 ( 991) hydrogen bonds : angle 4.12591 ( 2928) covalent geometry : bond 0.00333 (12783) covalent geometry : angle 0.54557 (17225) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 232 time to evaluate : 1.648 Fit side-chains revert: symmetry clash REVERT: A 49 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7499 (tp40) REVERT: B 47 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.6957 (mttm) REVERT: B 56 GLN cc_start: 0.7426 (mm-40) cc_final: 0.7085 (mm-40) REVERT: C 61 ARG cc_start: 0.7343 (ttp80) cc_final: 0.6864 (ttp-170) REVERT: C 68 GLN cc_start: 0.6916 (tm-30) cc_final: 0.6487 (tm-30) REVERT: C 72 ASP cc_start: 0.5251 (OUTLIER) cc_final: 0.4535 (p0) REVERT: C 92 ARG cc_start: 0.7741 (mtp85) cc_final: 0.7320 (mtt-85) REVERT: C 185 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.7825 (mpt) REVERT: C 187 LYS cc_start: 0.8436 (mppt) cc_final: 0.7533 (mmtt) REVERT: D 31 LYS cc_start: 0.8375 (mtmt) cc_final: 0.7591 (mmtt) REVERT: D 123 GLU cc_start: 0.7458 (pm20) cc_final: 0.6917 (tp30) REVERT: F 14 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7993 (tp) REVERT: F 108 ASP cc_start: 0.7549 (t70) cc_final: 0.7093 (t70) REVERT: F 125 GLU cc_start: 0.7296 (pm20) cc_final: 0.6942 (pm20) REVERT: F 129 GLU cc_start: 0.7710 (pt0) cc_final: 0.7252 (pp20) REVERT: F 226 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7133 (mm-30) REVERT: G 141 ARG cc_start: 0.8015 (mtm-85) cc_final: 0.7653 (mtm110) REVERT: H 303 MET cc_start: 0.5837 (tmm) cc_final: 0.5439 (tmm) REVERT: J 303 MET cc_start: 0.6446 (ttt) cc_final: 0.6125 (mpt) outliers start: 40 outliers final: 25 residues processed: 257 average time/residue: 1.4926 time to fit residues: 414.1264 Evaluate side-chains 261 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 231 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 171 MET Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain I residue 243 ILE Chi-restraints excluded: chain I residue 268 LYS Chi-restraints excluded: chain I residue 316 ILE Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 249 VAL Chi-restraints excluded: chain J residue 271 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 130 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 115 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 144 optimal weight: 8.9990 chunk 83 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN C 105 ASN D 29 ASN D 83 ASN D 174 ASN ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN ** J 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.197164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.127922 restraints weight = 10830.036| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.83 r_work: 0.3168 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12783 Z= 0.167 Angle : 0.574 10.173 17225 Z= 0.306 Chirality : 0.040 0.172 2012 Planarity : 0.005 0.058 2184 Dihedral : 4.596 56.084 1737 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.20 % Allowed : 26.71 % Favored : 70.09 % 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: 2.07 (0.21), residues: 1613 helix: 1.75 (0.14), residues: 1389 sheet: None (None), residues: 0 loop : -0.92 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 21 HIS 0.002 0.001 HIS G 142 PHE 0.023 0.002 PHE B 48 TYR 0.010 0.001 TYR F 110 ARG 0.013 0.000 ARG D 61 Details of bonding type rmsd hydrogen bonds : bond 0.04682 ( 991) hydrogen bonds : angle 4.20795 ( 2928) covalent geometry : bond 0.00381 (12783) covalent geometry : angle 0.57391 (17225) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15976.84 seconds wall clock time: 275 minutes 38.18 seconds (16538.18 seconds total)