Starting phenix.real_space_refine on Thu Jul 2 22:23:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7pmg_13532/07_2026/7pmg_13532.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pmg_13532/07_2026/7pmg_13532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7pmg_13532/07_2026/7pmg_13532.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7pmg_13532/07_2026/7pmg_13532.cif" model { file = "/net/cci-nas-00/data/ceres_data/7pmg_13532/07_2026/7pmg_13532.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pmg_13532/07_2026/7pmg_13532.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pmg_13532/07_2026/7pmg_13532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pmg_13532/07_2026/7pmg_13532.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 3 5.21 5 S 63 5.16 5 C 6482 2.51 5 N 1730 2.21 5 O 1906 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10189 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6105 Classifications: {'peptide': 747} Link IDs: {'PTRANS': 27, 'TRANS': 719} Chain breaks: 5 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.93, per 1000 atoms: 0.19 Number of scatterers: 10189 At special positions: 0 Unit cell: (103.4, 129.8, 155.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 63 16.00 P 5 15.00 Mg 3 11.99 O 1906 8.00 N 1730 7.00 C 6482 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 Links applied TRANS " TRP H 1 " - " ALA H 7 " " DTH H 4 " - " ALA H 3 " Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 342.8 milliseconds 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH H 4 " Number of C-beta restraints generated: 2382 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 14 sheets defined 55.2% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 73 through 77 removed outlier: 3.665A pdb=" N LEU A 77 " --> pdb=" O LEU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 95 removed outlier: 3.764A pdb=" N LYS A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 119 removed outlier: 4.213A pdb=" N TYR A 119 " --> pdb=" O LEU A 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 116 through 119' Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 138 through 153 removed outlier: 3.705A pdb=" N GLU A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 185 Processing helix chain 'A' and resid 191 through 207 removed outlier: 3.921A pdb=" N LYS A 195 " --> pdb=" O ASN A 191 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 259 through 269 removed outlier: 4.292A pdb=" N TYR A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 removed outlier: 4.412A pdb=" N THR A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 removed outlier: 4.057A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 315 removed outlier: 3.687A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 337 removed outlier: 3.701A pdb=" N ASN A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 365 Processing helix chain 'A' and resid 367 through 376 removed outlier: 4.092A pdb=" N CYS A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 424 Processing helix chain 'A' and resid 448 through 480 Processing helix chain 'A' and resid 483 through 487 removed outlier: 4.005A pdb=" N LEU A 486 " --> pdb=" O PRO A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 501 Processing helix chain 'A' and resid 504 through 515 removed outlier: 3.837A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 532 Processing helix chain 'A' and resid 563 through 568 Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.744A pdb=" N ILE A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A 582 " --> pdb=" O LYS A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 594 removed outlier: 4.133A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 653 Processing helix chain 'A' and resid 674 through 685 removed outlier: 3.741A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 696 removed outlier: 3.725A pdb=" N ARG A 692 " --> pdb=" O LEU A 688 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 696 " --> pdb=" O ARG A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 712 Processing helix chain 'A' and resid 713 through 715 No H-bonds generated for 'chain 'A' and resid 713 through 715' Processing helix chain 'A' and resid 723 through 736 removed outlier: 3.799A pdb=" N GLU A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 754 through 792 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.711A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.051A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.561A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 182 through 196 removed outlier: 3.801A pdb=" N THR C 186 " --> pdb=" O GLY C 182 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.702A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 removed outlier: 3.502A pdb=" N GLU C 226 " --> pdb=" O ASP C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 273 through 283 Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.518A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 4.288A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 348 through 349 No H-bonds generated for 'chain 'C' and resid 348 through 349' Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.794A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 4.296A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 19 Processing helix chain 'B' and resid 29 through 39 removed outlier: 4.243A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ASP B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 53 Processing helix chain 'B' and resid 56 through 63 Processing helix chain 'B' and resid 67 through 79 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 95 Processing helix chain 'B' and resid 105 through 116 Processing helix chain 'B' and resid 121 through 130 Processing helix chain 'B' and resid 140 through 150 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 16 removed outlier: 4.301A pdb=" N ALA A 11 " --> pdb=" O LEU A 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 103 removed outlier: 6.525A pdb=" N LEU A 107 " --> pdb=" O ARG A 660 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ILE A 662 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ALA A 109 " --> pdb=" O ILE A 662 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N SER A 158 " --> pdb=" O HIS A 657 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL A 659 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ILE A 160 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N CYS A 661 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N SER A 162 " --> pdb=" O CYS A 661 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLN A 157 " --> pdb=" O GLY A 434 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N LEU A 436 " --> pdb=" O GLN A 157 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE A 159 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ILE A 438 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N VAL A 161 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 211 removed outlier: 5.738A pdb=" N ALA A 209 " --> pdb=" O ASN A 216 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 341 through 342 Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 381 Processing sheet with id=AA6, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA7, first strand: chain 'A' and resid 700 through 703 Processing sheet with id=AA8, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.903A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB1, first strand: chain 'C' and resid 71 through 72 removed outlier: 3.657A pdb=" N ILE C 75 " --> pdb=" O GLU C 72 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.011A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB5, first strand: chain 'B' and resid 26 through 28 512 hydrogen bonds defined for protein. 1434 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.00 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1706 1.31 - 1.44: 2757 1.44 - 1.56: 5830 1.56 - 1.69: 8 1.69 - 1.82: 102 Bond restraints: 10403 Sorted by residual: bond pdb=" O3A ANP A1901 " pdb=" PB ANP A1901 " ideal model delta sigma weight residual 1.700 1.546 0.154 2.00e-02 2.50e+03 5.93e+01 bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.432 0.140 2.00e-02 2.50e+03 4.90e+01 bond pdb=" N3B ANP A1901 " pdb=" PG ANP A1901 " ideal model delta sigma weight residual 1.795 1.689 0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" O5' ANP A1901 " pdb=" PA ANP A1901 " ideal model delta sigma weight residual 1.655 1.564 0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" C EEP H 2 " pdb=" O EEP H 2 " ideal model delta sigma weight residual 1.263 1.189 0.074 2.00e-02 2.50e+03 1.36e+01 ... (remaining 10398 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.47: 13763 3.47 - 6.93: 266 6.93 - 10.40: 18 10.40 - 13.86: 5 13.86 - 17.33: 1 Bond angle restraints: 14053 Sorted by residual: angle pdb=" N GLY A 563 " pdb=" CA GLY A 563 " pdb=" C GLY A 563 " ideal model delta sigma weight residual 113.86 123.43 -9.57 1.50e+00 4.44e-01 4.07e+01 angle pdb=" C HYP H 6 " pdb=" N ALA H 7 " pdb=" CA ALA H 7 " ideal model delta sigma weight residual 121.70 111.27 10.43 1.80e+00 3.09e-01 3.35e+01 angle pdb=" PB ANP A1901 " pdb=" N3B ANP A1901 " pdb=" PG ANP A1901 " ideal model delta sigma weight residual 126.95 109.62 17.33 3.00e+00 1.11e-01 3.34e+01 angle pdb=" N DTH H 4 " pdb=" CA DTH H 4 " pdb=" CB DTH H 4 " ideal model delta sigma weight residual 111.50 102.04 9.46 1.70e+00 3.46e-01 3.10e+01 angle pdb=" CD2 TRP H 1 " pdb=" CE2 TRP H 1 " pdb=" CZ2 TRP H 1 " ideal model delta sigma weight residual 122.40 117.74 4.66 1.00e+00 1.00e+00 2.17e+01 ... (remaining 14048 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.62: 5983 24.62 - 49.24: 212 49.24 - 73.87: 40 73.87 - 98.49: 21 98.49 - 123.11: 5 Dihedral angle restraints: 6261 sinusoidal: 2567 harmonic: 3694 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 63.07 -123.08 1 2.00e+01 2.50e-03 3.71e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 61.08 -121.08 1 2.00e+01 2.50e-03 3.64e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 -178.23 118.24 1 2.00e+01 2.50e-03 3.54e+01 ... (remaining 6258 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.032: 1532 1.032 - 2.065: 0 2.065 - 3.097: 0 3.097 - 4.129: 0 4.129 - 5.161: 2 Chirality restraints: 1534 Sorted by residual: chirality pdb=" CB DTH H 4 " pdb=" CA DTH H 4 " pdb=" OG1 DTH H 4 " pdb=" CG2 DTH H 4 " both_signs ideal model delta sigma weight residual False 2.55 -2.61 5.16 2.00e-01 2.50e+01 6.66e+02 chirality pdb=" CA DTH H 4 " pdb=" N DTH H 4 " pdb=" C DTH H 4 " pdb=" CB DTH H 4 " both_signs ideal model delta sigma weight residual False 2.53 -2.37 4.89 2.00e-01 2.50e+01 5.99e+02 chirality pdb=" CA GLU C 316 " pdb=" N GLU C 316 " pdb=" C GLU C 316 " pdb=" CB GLU C 316 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 1531 not shown) Planarity restraints: 1794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 564 " -0.042 2.00e-02 2.50e+03 4.02e-02 2.83e+01 pdb=" CG PHE A 564 " 0.093 2.00e-02 2.50e+03 pdb=" CD1 PHE A 564 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE A 564 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 564 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 564 " -0.012 2.00e-02 2.50e+03 pdb=" CZ PHE A 564 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 278 " -0.134 9.50e-02 1.11e+02 7.49e-02 2.73e+01 pdb=" NE ARG A 278 " 0.037 2.00e-02 2.50e+03 pdb=" CZ ARG A 278 " -0.085 2.00e-02 2.50e+03 pdb=" NH1 ARG A 278 " 0.030 2.00e-02 2.50e+03 pdb=" NH2 ARG A 278 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 231 " 0.275 9.50e-02 1.11e+02 1.27e-01 2.07e+01 pdb=" NE ARG A 231 " 0.003 2.00e-02 2.50e+03 pdb=" CZ ARG A 231 " -0.062 2.00e-02 2.50e+03 pdb=" NH1 ARG A 231 " 0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG A 231 " 0.029 2.00e-02 2.50e+03 ... (remaining 1791 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.36: 19 2.36 - 3.00: 5722 3.00 - 3.63: 14764 3.63 - 4.27: 22880 4.27 - 4.90: 38604 Nonbonded interactions: 81989 Sorted by model distance: nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.727 3.620 nonbonded pdb=" O1B ANP A1901 " pdb="MG MG A1903 " model vdw 1.936 2.170 nonbonded pdb=" O1A ANP A1901 " pdb="MG MG A1903 " model vdw 1.948 2.170 nonbonded pdb=" O3G ANP A1901 " pdb="MG MG A1902 " model vdw 1.963 2.170 nonbonded pdb=" OH TYR A 456 " pdb=" OE1 GLU A 500 " model vdw 2.025 3.040 ... (remaining 81984 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 3.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.050 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 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 : 0.014 0.154 10405 Z= 0.620 Angle : 1.187 17.330 14059 Z= 0.662 Chirality : 0.194 5.161 1534 Planarity : 0.009 0.127 1792 Dihedral : 15.152 123.109 3873 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.09 % Allowed : 0.37 % Favored : 99.54 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.21), residues: 1235 helix: -1.69 (0.17), residues: 581 sheet: 0.25 (0.35), residues: 180 loop : 0.00 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.087 0.013 ARG A 278 TYR 0.032 0.007 TYR A 439 PHE 0.093 0.004 PHE A 564 TRP 0.052 0.006 TRP C 356 HIS 0.018 0.003 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.01445 / 0.62 (10403) covalent geometry : angle 1.18362 / 0.66 (14053) hydrogen bonds : bond 0.14129 / 9.16 ( 510) hydrogen bonds : angle 6.88607 / 4.62 ( 1434) link_TRANS : bond 0.02383 / 1.18 ( 2) link_TRANS : angle 4.22962 / 2.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 790 MET cc_start: 0.8908 (tpt) cc_final: 0.8655 (tpp) REVERT: C 41 GLN cc_start: 0.7833 (tt0) cc_final: 0.7598 (tt0) REVERT: B 73 MET cc_start: 0.9109 (mtp) cc_final: 0.8411 (ttm) outliers start: 1 outliers final: 1 residues processed: 93 average time/residue: 0.1263 time to fit residues: 15.8423 Evaluate side-chains 56 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 0.0050 chunk 33 optimal weight: 0.4980 chunk 123 optimal weight: 9.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 HIS A 200 ASN A 264 GLN A 398 ASN A 410 ASN A 493 GLN A 657 HIS A 775 GLN C 111 ASN C 137 GLN C 162 ASN C 280 ASN C 296 ASN B 75 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.047581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.034318 restraints weight = 54066.625| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 3.99 r_work: 0.2579 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10405 Z= 0.139 Angle : 0.659 7.557 14059 Z= 0.347 Chirality : 0.043 0.171 1534 Planarity : 0.004 0.042 1792 Dihedral : 9.800 128.184 1391 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 0.55 % Allowed : 3.23 % Favored : 96.22 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.23), residues: 1235 helix: 0.52 (0.20), residues: 602 sheet: 0.66 (0.37), residues: 182 loop : 0.56 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 64 TYR 0.017 0.002 TYR A 79 PHE 0.020 0.001 PHE C 255 TRP 0.021 0.002 TRP C 79 HIS 0.008 0.001 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (10403) covalent geometry : angle 0.65833 / 0.35 (14053) hydrogen bonds : bond 0.04200 / 2.67 ( 510) hydrogen bonds : angle 5.03566 / 3.41 ( 1434) link_TRANS : bond 0.00203 / 0.10 ( 2) link_TRANS : angle 1.45047 / 0.74 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 ASP cc_start: 0.8855 (t0) cc_final: 0.8398 (t0) REVERT: A 790 MET cc_start: 0.9062 (tpt) cc_final: 0.8842 (tpp) REVERT: C 106 THR cc_start: 0.9206 (m) cc_final: 0.8568 (p) REVERT: C 137 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8694 (mm110) REVERT: C 227 MET cc_start: 0.8187 (mmm) cc_final: 0.7954 (tpp) REVERT: C 364 GLU cc_start: 0.9131 (tm-30) cc_final: 0.8809 (pp20) REVERT: B 73 MET cc_start: 0.9254 (mtp) cc_final: 0.8545 (ttm) outliers start: 6 outliers final: 3 residues processed: 68 average time/residue: 0.1092 time to fit residues: 10.4500 Evaluate side-chains 60 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain B residue 111 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 64 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 0.0030 chunk 96 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 61 optimal weight: 0.4980 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 657 HIS C 111 ASN C 137 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.047061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.033770 restraints weight = 55086.555| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 4.01 r_work: 0.2564 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10405 Z= 0.156 Angle : 0.585 8.445 14059 Z= 0.304 Chirality : 0.042 0.176 1534 Planarity : 0.004 0.039 1792 Dihedral : 9.230 130.302 1390 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 0.55 % Allowed : 3.78 % Favored : 95.67 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.24), residues: 1235 helix: 1.20 (0.21), residues: 607 sheet: 0.91 (0.39), residues: 181 loop : 0.68 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 95 TYR 0.014 0.001 TYR A 102 PHE 0.015 0.001 PHE C 255 TRP 0.013 0.002 TRP C 79 HIS 0.006 0.001 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (10403) covalent geometry : angle 0.58495 / 0.30 (14053) hydrogen bonds : bond 0.03621 / 2.29 ( 510) hydrogen bonds : angle 4.72257 / 3.20 ( 1434) link_TRANS : bond 0.00378 / 0.19 ( 2) link_TRANS : angle 0.35983 / 0.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 478 MET cc_start: 0.9407 (mmp) cc_final: 0.9136 (mmp) REVERT: A 484 TRP cc_start: 0.8020 (m-90) cc_final: 0.7487 (m-90) REVERT: A 488 ASP cc_start: 0.8759 (t0) cc_final: 0.8459 (t0) REVERT: A 790 MET cc_start: 0.9132 (tpt) cc_final: 0.8922 (tpp) REVERT: C 227 MET cc_start: 0.8171 (mmm) cc_final: 0.7954 (tpp) REVERT: B 36 MET cc_start: 0.9217 (ttm) cc_final: 0.8892 (tpp) outliers start: 6 outliers final: 3 residues processed: 63 average time/residue: 0.1083 time to fit residues: 9.5943 Evaluate side-chains 56 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain B residue 111 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 8 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 111 optimal weight: 0.0060 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 657 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.046958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.033687 restraints weight = 55355.395| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 4.01 r_work: 0.2559 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10405 Z= 0.159 Angle : 0.579 8.169 14059 Z= 0.298 Chirality : 0.041 0.169 1534 Planarity : 0.004 0.038 1792 Dihedral : 8.965 129.623 1390 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.46 % Allowed : 4.52 % Favored : 95.02 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.24), residues: 1235 helix: 1.42 (0.21), residues: 606 sheet: 0.96 (0.39), residues: 179 loop : 0.58 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 95 TYR 0.013 0.001 TYR A 127 PHE 0.012 0.001 PHE C 255 TRP 0.011 0.001 TRP C 79 HIS 0.005 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (10403) covalent geometry : angle 0.57946 / 0.30 (14053) hydrogen bonds : bond 0.03443 / 2.18 ( 510) hydrogen bonds : angle 4.60738 / 3.12 ( 1434) link_TRANS : bond 0.00257 / 0.13 ( 2) link_TRANS : angle 0.35783 / 0.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 THR cc_start: 0.9120 (OUTLIER) cc_final: 0.8796 (p) REVERT: A 478 MET cc_start: 0.9402 (mmp) cc_final: 0.9074 (mmp) REVERT: A 484 TRP cc_start: 0.7973 (m-90) cc_final: 0.7364 (m-90) REVERT: A 488 ASP cc_start: 0.8820 (t0) cc_final: 0.8547 (t70) REVERT: C 227 MET cc_start: 0.8214 (mmm) cc_final: 0.7961 (tpp) REVERT: B 36 MET cc_start: 0.9235 (ttm) cc_final: 0.8838 (tpp) outliers start: 5 outliers final: 2 residues processed: 60 average time/residue: 0.1074 time to fit residues: 9.4286 Evaluate side-chains 55 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain B residue 111 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 11 optimal weight: 0.7980 chunk 114 optimal weight: 7.9990 chunk 87 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 120 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 657 HIS C 111 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.047378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.034328 restraints weight = 55460.966| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 4.05 r_work: 0.2570 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10405 Z= 0.123 Angle : 0.530 7.885 14059 Z= 0.271 Chirality : 0.040 0.167 1534 Planarity : 0.004 0.037 1792 Dihedral : 8.653 128.152 1390 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.55 % Allowed : 5.35 % Favored : 94.10 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.25), residues: 1235 helix: 1.65 (0.22), residues: 604 sheet: 0.78 (0.41), residues: 171 loop : 0.68 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 278 TYR 0.013 0.001 TYR A 102 PHE 0.010 0.001 PHE C 255 TRP 0.012 0.001 TRP A 781 HIS 0.004 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (10403) covalent geometry : angle 0.52992 / 0.27 (14053) hydrogen bonds : bond 0.03131 / 1.99 ( 510) hydrogen bonds : angle 4.43834 / 3.03 ( 1434) link_TRANS : bond 0.00171 / 0.09 ( 2) link_TRANS : angle 0.21144 / 0.10 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 THR cc_start: 0.9181 (OUTLIER) cc_final: 0.8894 (p) REVERT: A 382 THR cc_start: 0.9214 (OUTLIER) cc_final: 0.8883 (p) REVERT: A 478 MET cc_start: 0.9418 (mmp) cc_final: 0.9042 (mmp) REVERT: A 488 ASP cc_start: 0.8882 (t0) cc_final: 0.8611 (t70) REVERT: C 227 MET cc_start: 0.8243 (mmm) cc_final: 0.7981 (tpp) REVERT: B 36 MET cc_start: 0.9247 (ttm) cc_final: 0.8811 (tpp) outliers start: 6 outliers final: 4 residues processed: 63 average time/residue: 0.0940 time to fit residues: 8.7868 Evaluate side-chains 60 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain B residue 111 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 11 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 2 optimal weight: 0.0470 chunk 119 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 overall best weight: 2.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 657 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.046116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.032810 restraints weight = 56139.951| |-----------------------------------------------------------------------------| r_work (start): 0.2695 rms_B_bonded: 4.00 r_work: 0.2526 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 10405 Z= 0.242 Angle : 0.609 8.488 14059 Z= 0.307 Chirality : 0.042 0.165 1534 Planarity : 0.004 0.035 1792 Dihedral : 8.619 131.234 1390 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.74 % Allowed : 5.81 % Favored : 93.46 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.25), residues: 1235 helix: 1.72 (0.22), residues: 606 sheet: 0.93 (0.40), residues: 184 loop : 0.56 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 278 TYR 0.013 0.001 TYR A 456 PHE 0.013 0.001 PHE C 255 TRP 0.011 0.002 TRP C 79 HIS 0.005 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.24 (10403) covalent geometry : angle 0.60902 / 0.31 (14053) hydrogen bonds : bond 0.03441 / 2.15 ( 510) hydrogen bonds : angle 4.51985 / 3.08 ( 1434) link_TRANS : bond 0.00400 / 0.20 ( 2) link_TRANS : angle 0.47900 / 0.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 THR cc_start: 0.9223 (OUTLIER) cc_final: 0.8904 (p) REVERT: A 382 THR cc_start: 0.9219 (OUTLIER) cc_final: 0.8878 (p) REVERT: A 488 ASP cc_start: 0.8827 (t0) cc_final: 0.8550 (t70) REVERT: C 227 MET cc_start: 0.8362 (mmm) cc_final: 0.8022 (tpp) REVERT: B 36 MET cc_start: 0.9310 (ttm) cc_final: 0.8766 (tpp) outliers start: 8 outliers final: 3 residues processed: 58 average time/residue: 0.1060 time to fit residues: 9.1340 Evaluate side-chains 55 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain B residue 111 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 113 optimal weight: 7.9990 chunk 60 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 106 optimal weight: 0.1980 chunk 77 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 123 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 HIS C 111 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.046886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.033581 restraints weight = 55013.370| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 4.00 r_work: 0.2562 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10405 Z= 0.128 Angle : 0.537 9.414 14059 Z= 0.269 Chirality : 0.040 0.165 1534 Planarity : 0.004 0.035 1792 Dihedral : 8.400 134.856 1390 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.65 % Allowed : 6.36 % Favored : 93.00 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.25), residues: 1235 helix: 1.87 (0.22), residues: 601 sheet: 0.76 (0.41), residues: 173 loop : 0.64 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 278 TYR 0.010 0.001 TYR A 456 PHE 0.010 0.001 PHE C 255 TRP 0.019 0.002 TRP A 484 HIS 0.004 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (10403) covalent geometry : angle 0.53661 / 0.27 (14053) hydrogen bonds : bond 0.03102 / 1.97 ( 510) hydrogen bonds : angle 4.37802 / 2.99 ( 1434) link_TRANS : bond 0.00175 / 0.09 ( 2) link_TRANS : angle 0.26102 / 0.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 THR cc_start: 0.9240 (OUTLIER) cc_final: 0.8933 (p) REVERT: A 382 THR cc_start: 0.9224 (OUTLIER) cc_final: 0.8870 (p) REVERT: A 484 TRP cc_start: 0.8241 (m-90) cc_final: 0.7777 (m-90) REVERT: A 488 ASP cc_start: 0.8851 (t0) cc_final: 0.8572 (t70) REVERT: C 227 MET cc_start: 0.8325 (mmm) cc_final: 0.8013 (tpp) REVERT: B 36 MET cc_start: 0.9227 (ttm) cc_final: 0.8684 (tpp) outliers start: 7 outliers final: 2 residues processed: 59 average time/residue: 0.0920 time to fit residues: 8.2833 Evaluate side-chains 55 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain B residue 111 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 65 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.045796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.032486 restraints weight = 55942.362| |-----------------------------------------------------------------------------| r_work (start): 0.2684 rms_B_bonded: 3.99 r_work: 0.2513 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 10405 Z= 0.238 Angle : 0.595 9.342 14059 Z= 0.300 Chirality : 0.042 0.167 1534 Planarity : 0.004 0.035 1792 Dihedral : 8.455 140.243 1390 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.55 % Allowed : 6.73 % Favored : 92.72 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.25), residues: 1235 helix: 1.75 (0.22), residues: 612 sheet: 0.76 (0.42), residues: 163 loop : 0.47 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 278 TYR 0.013 0.001 TYR A 10 PHE 0.014 0.001 PHE A 564 TRP 0.018 0.002 TRP A 484 HIS 0.005 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.24 (10403) covalent geometry : angle 0.59500 / 0.30 (14053) hydrogen bonds : bond 0.03486 / 2.18 ( 510) hydrogen bonds : angle 4.49915 / 3.06 ( 1434) link_TRANS : bond 0.00440 / 0.22 ( 2) link_TRANS : angle 0.45340 / 0.22 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 THR cc_start: 0.9261 (OUTLIER) cc_final: 0.8937 (p) REVERT: A 382 THR cc_start: 0.9227 (OUTLIER) cc_final: 0.8873 (p) REVERT: A 488 ASP cc_start: 0.8793 (t0) cc_final: 0.8473 (t70) REVERT: C 227 MET cc_start: 0.8441 (mmm) cc_final: 0.8106 (tpp) REVERT: C 311 ASP cc_start: 0.9158 (t0) cc_final: 0.8913 (t0) REVERT: B 36 MET cc_start: 0.9262 (ttm) cc_final: 0.8702 (tpp) outliers start: 6 outliers final: 3 residues processed: 59 average time/residue: 0.0963 time to fit residues: 8.6495 Evaluate side-chains 57 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain B residue 111 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 22 optimal weight: 0.1980 chunk 106 optimal weight: 0.0980 chunk 68 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.046835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.033497 restraints weight = 55583.455| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 4.04 r_work: 0.2556 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10405 Z= 0.110 Angle : 0.540 10.173 14059 Z= 0.268 Chirality : 0.040 0.165 1534 Planarity : 0.003 0.036 1792 Dihedral : 8.281 143.558 1390 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.37 % Allowed : 6.91 % Favored : 92.72 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.25), residues: 1235 helix: 1.87 (0.22), residues: 608 sheet: 0.76 (0.42), residues: 168 loop : 0.54 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 278 TYR 0.013 0.001 TYR A 102 PHE 0.009 0.001 PHE C 255 TRP 0.023 0.002 TRP A 484 HIS 0.003 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (10403) covalent geometry : angle 0.54010 / 0.27 (14053) hydrogen bonds : bond 0.03052 / 1.93 ( 510) hydrogen bonds : angle 4.34720 / 2.97 ( 1434) link_TRANS : bond 0.00141 / 0.07 ( 2) link_TRANS : angle 0.21961 / 0.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 THR cc_start: 0.9246 (OUTLIER) cc_final: 0.8953 (p) REVERT: A 382 THR cc_start: 0.9192 (OUTLIER) cc_final: 0.8823 (p) REVERT: A 488 ASP cc_start: 0.8833 (t0) cc_final: 0.8569 (t70) REVERT: C 227 MET cc_start: 0.8354 (mmm) cc_final: 0.8058 (tpp) REVERT: C 311 ASP cc_start: 0.9102 (t0) cc_final: 0.8831 (t0) REVERT: B 36 MET cc_start: 0.9160 (ttm) cc_final: 0.8667 (tpp) outliers start: 4 outliers final: 2 residues processed: 58 average time/residue: 0.0943 time to fit residues: 8.4212 Evaluate side-chains 57 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain B residue 111 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 103 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 8 optimal weight: 0.0970 chunk 23 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 50 optimal weight: 0.0570 chunk 97 optimal weight: 0.0980 chunk 62 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.047536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.034736 restraints weight = 53757.405| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 3.84 r_work: 0.2590 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10405 Z= 0.095 Angle : 0.544 10.344 14059 Z= 0.268 Chirality : 0.039 0.166 1534 Planarity : 0.003 0.034 1792 Dihedral : 8.103 144.454 1390 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.37 % Allowed : 7.10 % Favored : 92.53 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.25), residues: 1235 helix: 1.90 (0.22), residues: 609 sheet: 0.81 (0.42), residues: 167 loop : 0.63 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 712 TYR 0.011 0.001 TYR A 711 PHE 0.010 0.001 PHE B 144 TRP 0.032 0.002 TRP A 484 HIS 0.003 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.09 (10403) covalent geometry : angle 0.54429 / 0.27 (14053) hydrogen bonds : bond 0.02894 / 1.85 ( 510) hydrogen bonds : angle 4.24243 / 2.91 ( 1434) link_TRANS : bond 0.00063 / 0.03 ( 2) link_TRANS : angle 0.14339 / 0.07 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2470 Ramachandran restraints generated. 1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.9380 (ptp) cc_final: 0.9031 (pmm) REVERT: A 211 THR cc_start: 0.9243 (OUTLIER) cc_final: 0.8987 (p) REVERT: A 382 THR cc_start: 0.9185 (OUTLIER) cc_final: 0.8825 (p) REVERT: A 488 ASP cc_start: 0.8838 (t0) cc_final: 0.8602 (t70) REVERT: C 227 MET cc_start: 0.8271 (mmm) cc_final: 0.7986 (tpp) REVERT: C 311 ASP cc_start: 0.9068 (t0) cc_final: 0.8794 (t0) REVERT: B 36 MET cc_start: 0.9026 (ttm) cc_final: 0.8503 (tpp) outliers start: 4 outliers final: 2 residues processed: 60 average time/residue: 0.0971 time to fit residues: 8.7657 Evaluate side-chains 56 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain B residue 111 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 6 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.046298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.032989 restraints weight = 55656.029| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 4.00 r_work: 0.2532 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10405 Z= 0.186 Angle : 0.573 10.374 14059 Z= 0.284 Chirality : 0.041 0.168 1534 Planarity : 0.004 0.036 1792 Dihedral : 8.204 149.802 1390 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.46 % Allowed : 6.91 % Favored : 92.63 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.25), residues: 1235 helix: 1.88 (0.22), residues: 609 sheet: 0.73 (0.43), residues: 158 loop : 0.55 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 278 TYR 0.011 0.001 TYR A 456 PHE 0.011 0.001 PHE C 255 TRP 0.037 0.002 TRP A 484 HIS 0.004 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 (10403) covalent geometry : angle 0.57302 / 0.28 (14053) hydrogen bonds : bond 0.03220 / 2.02 ( 510) hydrogen bonds : angle 4.33579 / 2.95 ( 1434) link_TRANS : bond 0.00313 / 0.16 ( 2) link_TRANS : angle 0.34879 / 0.16 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2223.33 seconds wall clock time: 39 minutes 3.22 seconds (2343.22 seconds total)