Starting phenix.real_space_refine on Wed Mar 4 03:51:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pmg_13532/03_2026/7pmg_13532.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pmg_13532/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7pmg_13532/03_2026/7pmg_13532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pmg_13532/03_2026/7pmg_13532.map" model { file = "/net/cci-nas-00/data/ceres_data/7pmg_13532/03_2026/7pmg_13532.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pmg_13532/03_2026/7pmg_13532.cif" } 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-5986/lib/python3.9/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 Unresolved non-hydrogen dihedrals: 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} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} 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: 2.57, per 1000 atoms: 0.25 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: 0.97 Conformation dependent library (CDL) restraints added in 522.3 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: 0.38 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: 1.47 Time building geometry restraints manager: 1.23 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: 5996 24.62 - 49.24: 224 49.24 - 73.87: 51 73.87 - 98.49: 23 98.49 - 123.11: 5 Dihedral angle restraints: 6299 sinusoidal: 2605 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 6296 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 942 0.058 - 0.117: 457 0.117 - 0.175: 113 0.175 - 0.234: 19 0.234 - 0.292: 3 Chirality restraints: 1534 Sorted by residual: 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 chirality pdb=" C3' ANP A1901 " pdb=" C2' ANP A1901 " pdb=" C4' ANP A1901 " pdb=" O3' ANP A1901 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" C2' ADP C 401 " pdb=" C1' ADP C 401 " pdb=" C3' ADP C 401 " pdb=" O2' ADP C 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.79 0.28 2.00e-01 2.50e+01 1.90e+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: 0.000 Normalize map: mean=0, sd=1: 2.860 Set stop_for_unknowns flag: 0.010 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.810 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 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 : 0.069 0.292 1534 Planarity : 0.009 0.127 1792 Dihedral : 15.701 123.109 3911 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 covalent geometry : bond 0.01445 (10403) covalent geometry : angle 1.18362 (14053) hydrogen bonds : bond 0.14129 ( 510) hydrogen bonds : angle 6.88607 ( 1434) link_TRANS : bond 0.02383 ( 2) link_TRANS : angle 4.22962 ( 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 : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 790 MET cc_start: 0.8908 (tpt) cc_final: 0.8654 (tpp) REVERT: C 41 GLN cc_start: 0.7833 (tt0) cc_final: 0.7597 (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: 0.1326 time to fit residues: 16.7158 Evaluate side-chains 55 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 81 HIS A 200 ASN A 264 GLN A 398 ASN A 493 GLN 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.047404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.034097 restraints weight = 53317.519| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 4.02 r_work: 0.2559 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10405 Z= 0.140 Angle : 0.674 7.573 14059 Z= 0.353 Chirality : 0.043 0.182 1534 Planarity : 0.004 0.041 1792 Dihedral : 11.376 127.793 1429 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.55 % Allowed : 3.69 % Favored : 95.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.67 (0.23), residues: 1235 helix: 0.50 (0.20), residues: 601 sheet: 0.66 (0.37), residues: 182 loop : 0.54 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 64 TYR 0.016 0.002 TYR A 79 PHE 0.022 0.001 PHE A 564 TRP 0.022 0.002 TRP C 79 HIS 0.008 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00303 (10403) covalent geometry : angle 0.67353 (14053) hydrogen bonds : bond 0.04276 ( 510) hydrogen bonds : angle 5.08147 ( 1434) link_TRANS : bond 0.00554 ( 2) link_TRANS : angle 1.16152 ( 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 64 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 ASP cc_start: 0.8871 (t0) cc_final: 0.8481 (t0) REVERT: A 790 MET cc_start: 0.9057 (tpt) cc_final: 0.8836 (tpp) REVERT: C 106 THR cc_start: 0.9216 (m) cc_final: 0.8916 (p) REVERT: C 137 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8633 (mm-40) REVERT: C 227 MET cc_start: 0.8185 (mmm) cc_final: 0.7973 (tpp) REVERT: C 364 GLU cc_start: 0.9090 (tm-30) cc_final: 0.8778 (pp20) REVERT: B 54 ASN cc_start: 0.9185 (m-40) cc_final: 0.8955 (m110) outliers start: 6 outliers final: 3 residues processed: 63 average time/residue: 0.1102 time to fit residues: 9.9172 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 : 0.381 ------------------------------------------------------------------------------- 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: 3.9990 chunk 29 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 0.0020 chunk 96 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 111 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN 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 = 0.3227 r_free = 0.3227 target = 0.047089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.033622 restraints weight = 54709.490| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 4.10 r_work: 0.2544 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2297 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= 0.145 Angle : 0.588 6.601 14059 Z= 0.303 Chirality : 0.042 0.175 1534 Planarity : 0.004 0.036 1792 Dihedral : 10.046 130.877 1428 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 0.55 % Allowed : 4.15 % Favored : 95.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.33 (0.24), residues: 1235 helix: 1.20 (0.21), residues: 609 sheet: 0.83 (0.40), residues: 170 loop : 0.70 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 147 TYR 0.016 0.001 TYR A 102 PHE 0.013 0.001 PHE A 564 TRP 0.015 0.002 TRP A 484 HIS 0.006 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00323 (10403) covalent geometry : angle 0.58743 (14053) hydrogen bonds : bond 0.03540 ( 510) hydrogen bonds : angle 4.69683 ( 1434) link_TRANS : bond 0.00178 ( 2) link_TRANS : angle 0.79083 ( 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 63 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 MET cc_start: 0.9273 (mmp) cc_final: 0.9070 (mmp) REVERT: A 488 ASP cc_start: 0.8785 (t0) cc_final: 0.8486 (t0) REVERT: A 790 MET cc_start: 0.9129 (tpt) cc_final: 0.8916 (tpp) REVERT: C 227 MET cc_start: 0.8156 (mmm) cc_final: 0.7937 (tpp) REVERT: B 36 MET cc_start: 0.9255 (ttm) cc_final: 0.8911 (tpp) outliers start: 6 outliers final: 2 residues processed: 61 average time/residue: 0.1049 time to fit residues: 9.2402 Evaluate side-chains 54 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 82 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.046251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.032848 restraints weight = 55656.088| |-----------------------------------------------------------------------------| r_work (start): 0.2696 rms_B_bonded: 4.09 r_work: 0.2517 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10405 Z= 0.214 Angle : 0.604 8.719 14059 Z= 0.308 Chirality : 0.042 0.169 1534 Planarity : 0.004 0.036 1792 Dihedral : 9.606 132.507 1428 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.74 % Allowed : 4.98 % Favored : 94.29 % Cbeta Deviations : 0.00 % 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: 1.54 (0.25), residues: 1235 helix: 1.53 (0.22), residues: 599 sheet: 0.94 (0.40), residues: 180 loop : 0.55 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 95 TYR 0.012 0.001 TYR A 456 PHE 0.013 0.001 PHE A 564 TRP 0.013 0.002 TRP A 484 HIS 0.006 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00480 (10403) covalent geometry : angle 0.60347 (14053) hydrogen bonds : bond 0.03601 ( 510) hydrogen bonds : angle 4.66734 ( 1434) link_TRANS : bond 0.00315 ( 2) link_TRANS : angle 0.81516 ( 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 63 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 THR cc_start: 0.9143 (OUTLIER) cc_final: 0.8799 (p) REVERT: A 488 ASP cc_start: 0.8837 (t0) cc_final: 0.8561 (t70) REVERT: C 227 MET cc_start: 0.8289 (mmm) cc_final: 0.7998 (tpp) REVERT: B 36 MET cc_start: 0.9240 (ttm) cc_final: 0.8834 (tpp) outliers start: 8 outliers final: 5 residues processed: 61 average time/residue: 0.1151 time to fit residues: 9.8211 Evaluate side-chains 58 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain B residue 73 MET 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: 0.9980 chunk 114 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.046493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.033225 restraints weight = 55389.419| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 4.00 r_work: 0.2543 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10405 Z= 0.151 Angle : 0.552 8.230 14059 Z= 0.280 Chirality : 0.041 0.169 1534 Planarity : 0.004 0.038 1792 Dihedral : 9.280 136.958 1428 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.74 % Allowed : 5.35 % Favored : 93.92 % Cbeta Deviations : 0.00 % 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: 599 sheet: 0.94 (0.40), residues: 182 loop : 0.58 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 278 TYR 0.011 0.001 TYR A 102 PHE 0.010 0.001 PHE C 255 TRP 0.019 0.002 TRP A 484 HIS 0.005 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00340 (10403) covalent geometry : angle 0.55156 (14053) hydrogen bonds : bond 0.03302 ( 510) hydrogen bonds : angle 4.50356 ( 1434) link_TRANS : bond 0.00214 ( 2) link_TRANS : angle 0.81822 ( 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 63 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 THR cc_start: 0.9192 (OUTLIER) cc_final: 0.8887 (p) REVERT: A 382 THR cc_start: 0.9212 (OUTLIER) cc_final: 0.8884 (p) REVERT: A 484 TRP cc_start: 0.8039 (m-90) cc_final: 0.7791 (m-90) REVERT: A 488 ASP cc_start: 0.8839 (t0) cc_final: 0.8560 (t70) REVERT: A 783 MET cc_start: 0.9268 (ppp) cc_final: 0.8888 (ppp) REVERT: A 788 MET cc_start: 0.7884 (mtt) cc_final: 0.7341 (tpp) REVERT: C 227 MET cc_start: 0.8299 (mmm) cc_final: 0.8039 (tpp) REVERT: B 36 MET cc_start: 0.9202 (ttm) cc_final: 0.8726 (tpp) outliers start: 8 outliers final: 4 residues processed: 61 average time/residue: 0.0901 time to fit residues: 8.2059 Evaluate side-chains 57 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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: 0.6980 chunk 61 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 119 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 120 optimal weight: 10.0000 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.046149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.032853 restraints weight = 56056.606| |-----------------------------------------------------------------------------| r_work (start): 0.2695 rms_B_bonded: 4.02 r_work: 0.2519 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 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 : 0.004 0.033 10405 Z= 0.196 Angle : 0.577 8.759 14059 Z= 0.290 Chirality : 0.041 0.170 1534 Planarity : 0.004 0.033 1792 Dihedral : 9.176 140.329 1428 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.92 % Allowed : 6.27 % Favored : 92.81 % Cbeta Deviations : 0.00 % 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: 1.81 (0.25), residues: 1235 helix: 1.84 (0.22), residues: 599 sheet: 0.94 (0.40), residues: 183 loop : 0.59 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 278 TYR 0.011 0.001 TYR A 456 PHE 0.011 0.001 PHE C 255 TRP 0.015 0.002 TRP A 484 HIS 0.005 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00442 (10403) covalent geometry : angle 0.57716 (14053) hydrogen bonds : bond 0.03354 ( 510) hydrogen bonds : angle 4.48680 ( 1434) link_TRANS : bond 0.00239 ( 2) link_TRANS : angle 0.76729 ( 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 60 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 THR cc_start: 0.9213 (OUTLIER) cc_final: 0.8893 (p) REVERT: A 382 THR cc_start: 0.9217 (OUTLIER) cc_final: 0.8879 (p) REVERT: A 488 ASP cc_start: 0.8822 (t0) cc_final: 0.8558 (t70) REVERT: A 783 MET cc_start: 0.9287 (ppp) cc_final: 0.8897 (ppp) REVERT: C 227 MET cc_start: 0.8330 (mmm) cc_final: 0.8038 (tpp) REVERT: B 36 MET cc_start: 0.9210 (ttm) cc_final: 0.8729 (tpp) outliers start: 10 outliers final: 5 residues processed: 57 average time/residue: 0.0910 time to fit residues: 8.1012 Evaluate side-chains 56 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 A residue 587 LYS Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain B residue 73 MET 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: 10.0000 chunk 60 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 118 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 123 optimal weight: 9.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3202 r_free = 0.3202 target = 0.046050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.032783 restraints weight = 55591.859| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 3.95 r_work: 0.2518 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 10405 Z= 0.189 Angle : 0.569 8.893 14059 Z= 0.286 Chirality : 0.041 0.170 1534 Planarity : 0.004 0.033 1792 Dihedral : 9.069 146.942 1428 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.83 % Allowed : 6.45 % Favored : 92.72 % Cbeta Deviations : 0.00 % 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: 1.79 (0.25), residues: 1235 helix: 1.81 (0.22), residues: 611 sheet: 0.89 (0.40), residues: 183 loop : 0.60 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 278 TYR 0.017 0.001 TYR A 127 PHE 0.013 0.001 PHE A 564 TRP 0.022 0.002 TRP A 484 HIS 0.004 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00425 (10403) covalent geometry : angle 0.56865 (14053) hydrogen bonds : bond 0.03342 ( 510) hydrogen bonds : angle 4.45451 ( 1434) link_TRANS : bond 0.00211 ( 2) link_TRANS : angle 0.75903 ( 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: 9 poor density : 50 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 THR cc_start: 0.9246 (OUTLIER) cc_final: 0.8913 (p) REVERT: A 382 THR cc_start: 0.9225 (OUTLIER) cc_final: 0.8866 (p) REVERT: A 488 ASP cc_start: 0.8828 (t0) cc_final: 0.8568 (t70) REVERT: C 227 MET cc_start: 0.8394 (mmm) cc_final: 0.8074 (tpp) REVERT: B 36 MET cc_start: 0.9169 (ttm) cc_final: 0.8735 (tpp) outliers start: 9 outliers final: 6 residues processed: 56 average time/residue: 0.0960 time to fit residues: 8.2159 Evaluate side-chains 57 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 A residue 587 LYS Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain B residue 73 MET 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: 0.0980 chunk 32 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 111 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.046507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.033188 restraints weight = 55571.796| |-----------------------------------------------------------------------------| r_work (start): 0.2703 rms_B_bonded: 4.01 r_work: 0.2534 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10405 Z= 0.130 Angle : 0.567 9.767 14059 Z= 0.284 Chirality : 0.040 0.168 1534 Planarity : 0.003 0.034 1792 Dihedral : 8.984 151.230 1428 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.74 % Allowed : 7.00 % Favored : 92.26 % Cbeta Deviations : 0.00 % 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: 1.84 (0.25), residues: 1235 helix: 1.92 (0.22), residues: 607 sheet: 0.76 (0.41), residues: 173 loop : 0.59 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 278 TYR 0.013 0.001 TYR A 127 PHE 0.008 0.001 PHE C 255 TRP 0.030 0.002 TRP A 484 HIS 0.004 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00291 (10403) covalent geometry : angle 0.56678 (14053) hydrogen bonds : bond 0.03128 ( 510) hydrogen bonds : angle 4.41758 ( 1434) link_TRANS : bond 0.00166 ( 2) link_TRANS : angle 0.80539 ( 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 60 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.8897 (ppp) cc_final: 0.8669 (ppp) REVERT: A 177 MET cc_start: 0.9496 (ptp) cc_final: 0.9065 (pmm) REVERT: A 211 THR cc_start: 0.9234 (OUTLIER) cc_final: 0.8930 (p) REVERT: A 382 THR cc_start: 0.9169 (OUTLIER) cc_final: 0.8784 (p) REVERT: A 488 ASP cc_start: 0.8803 (t0) cc_final: 0.8536 (t70) REVERT: C 227 MET cc_start: 0.8341 (mmm) cc_final: 0.8012 (tpp) REVERT: B 36 MET cc_start: 0.9122 (ttm) cc_final: 0.8678 (tpp) outliers start: 8 outliers final: 3 residues processed: 57 average time/residue: 0.0859 time to fit residues: 7.5432 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 : 0.391 ------------------------------------------------------------------------------- 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 305 MET 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: 0.6980 chunk 47 optimal weight: 0.0770 chunk 117 optimal weight: 8.9990 chunk 22 optimal weight: 0.7980 chunk 106 optimal weight: 0.3980 chunk 68 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.046999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.033661 restraints weight = 55598.149| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 4.04 r_work: 0.2551 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10405 Z= 0.105 Angle : 0.550 10.073 14059 Z= 0.272 Chirality : 0.040 0.167 1534 Planarity : 0.003 0.033 1792 Dihedral : 8.807 155.342 1428 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.65 % Allowed : 7.56 % Favored : 91.80 % Cbeta Deviations : 0.00 % 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: 1.88 (0.25), residues: 1235 helix: 1.99 (0.22), residues: 603 sheet: 0.74 (0.41), residues: 173 loop : 0.59 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 278 TYR 0.011 0.001 TYR A 102 PHE 0.008 0.001 PHE B 16 TRP 0.029 0.002 TRP A 484 HIS 0.003 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00231 (10403) covalent geometry : angle 0.54948 (14053) hydrogen bonds : bond 0.02932 ( 510) hydrogen bonds : angle 4.32417 ( 1434) link_TRANS : bond 0.00173 ( 2) link_TRANS : angle 0.81660 ( 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 61 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 THR cc_start: 0.9240 (OUTLIER) cc_final: 0.8960 (p) REVERT: A 382 THR cc_start: 0.9185 (OUTLIER) cc_final: 0.8814 (p) REVERT: A 515 MET cc_start: 0.9271 (tpp) cc_final: 0.9067 (tpt) REVERT: A 689 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8528 (tp30) REVERT: A 788 MET cc_start: 0.8294 (ptp) cc_final: 0.7870 (tpp) REVERT: C 227 MET cc_start: 0.8288 (mmm) cc_final: 0.8008 (tpp) REVERT: C 311 ASP cc_start: 0.9107 (t0) cc_final: 0.8868 (t0) REVERT: B 36 MET cc_start: 0.9083 (ttm) cc_final: 0.8581 (tpp) outliers start: 7 outliers final: 3 residues processed: 58 average time/residue: 0.0923 time to fit residues: 8.2869 Evaluate side-chains 54 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 689 GLU Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain B residue 73 MET 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: 3.9990 chunk 56 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 1 optimal weight: 0.0170 chunk 8 optimal weight: 0.0370 chunk 23 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 70 optimal weight: 3.9990 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.047230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.034198 restraints weight = 53545.168| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 3.96 r_work: 0.2565 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10405 Z= 0.099 Angle : 0.549 10.649 14059 Z= 0.270 Chirality : 0.040 0.217 1534 Planarity : 0.003 0.033 1792 Dihedral : 8.673 158.650 1428 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.46 % Allowed : 7.47 % Favored : 92.07 % Cbeta Deviations : 0.00 % 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: 1.98 (0.25), residues: 1235 helix: 2.04 (0.22), residues: 603 sheet: 0.92 (0.41), residues: 170 loop : 0.63 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 278 TYR 0.018 0.001 TYR A 127 PHE 0.009 0.001 PHE B 144 TRP 0.028 0.002 TRP A 484 HIS 0.003 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00219 (10403) covalent geometry : angle 0.54888 (14053) hydrogen bonds : bond 0.02908 ( 510) hydrogen bonds : angle 4.28166 ( 1434) link_TRANS : bond 0.00175 ( 2) link_TRANS : angle 0.80969 ( 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 56 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8252 (tpt) cc_final: 0.8023 (tpp) REVERT: A 177 MET cc_start: 0.9540 (ptp) cc_final: 0.9243 (pmm) REVERT: A 211 THR cc_start: 0.9240 (OUTLIER) cc_final: 0.8981 (p) REVERT: A 382 THR cc_start: 0.9167 (OUTLIER) cc_final: 0.8784 (p) REVERT: A 788 MET cc_start: 0.8293 (ptp) cc_final: 0.7949 (tpp) REVERT: C 227 MET cc_start: 0.8246 (mmm) cc_final: 0.7961 (tpp) REVERT: B 36 MET cc_start: 0.9017 (ttm) cc_final: 0.8493 (tpp) outliers start: 5 outliers final: 3 residues processed: 54 average time/residue: 0.0938 time to fit residues: 7.7973 Evaluate side-chains 54 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 305 MET Chi-restraints excluded: chain B residue 73 MET 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: 5.9990 chunk 45 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 120 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.046891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.033872 restraints weight = 54595.345| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 3.99 r_work: 0.2554 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10405 Z= 0.121 Angle : 0.566 10.658 14059 Z= 0.276 Chirality : 0.040 0.190 1534 Planarity : 0.003 0.035 1792 Dihedral : 8.636 161.142 1428 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.46 % Allowed : 7.65 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.98 (0.25), residues: 1235 helix: 2.03 (0.22), residues: 610 sheet: 0.85 (0.41), residues: 160 loop : 0.65 (0.31), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 278 TYR 0.014 0.001 TYR A 127 PHE 0.009 0.001 PHE C 255 TRP 0.025 0.002 TRP A 484 HIS 0.003 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00274 (10403) covalent geometry : angle 0.56546 (14053) hydrogen bonds : bond 0.02919 ( 510) hydrogen bonds : angle 4.26891 ( 1434) link_TRANS : bond 0.00154 ( 2) link_TRANS : angle 0.75913 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2341.60 seconds wall clock time: 40 minutes 56.37 seconds (2456.37 seconds total)