Starting phenix.real_space_refine on Fri Feb 6 05:15:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h89_51933/02_2026/9h89_51933_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h89_51933/02_2026/9h89_51933.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9h89_51933/02_2026/9h89_51933.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h89_51933/02_2026/9h89_51933.map" model { file = "/net/cci-nas-00/data/ceres_data/9h89_51933/02_2026/9h89_51933_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h89_51933/02_2026/9h89_51933_neut.cif" } resolution = 4.0 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= 0.002 sd= 0.016 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: 5 Type Number sf(0) Gaussians S 32 5.16 5 C 7232 2.51 5 N 1955 2.21 5 O 2263 1.98 5 H 11052 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22534 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 11174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 11174 Classifications: {'peptide': 723} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 694} Chain: "B" Number of atoms: 5534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 5534 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 359} Chain: "C" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 963 Classifications: {'peptide': 67} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 59} Chain: "D" Number of atoms: 3460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3460 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "E" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1403 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 85} Time building chain proxies: 3.17, per 1000 atoms: 0.14 Number of scatterers: 22534 At special positions: 0 Unit cell: (142.87, 100.1, 117.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 O 2263 8.00 N 1955 7.00 C 7232 6.00 H 11052 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.93 Conformation dependent library (CDL) restraints added in 783.9 milliseconds 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2686 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 15 sheets defined 24.4% alpha, 29.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 106 through 118 removed outlier: 3.603A pdb=" N LEU A 110 " --> pdb=" O LYS A 106 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS A 111 " --> pdb=" O ASP A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 144 removed outlier: 3.978A pdb=" N LYS A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLY A 136 " --> pdb=" O ASP A 132 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.761A pdb=" N LEU A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N HIS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 234 Processing helix chain 'A' and resid 280 through 289 Processing helix chain 'A' and resid 297 through 316 Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.945A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 393 removed outlier: 3.792A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.761A pdb=" N TYR A 548 " --> pdb=" O ALA A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 624 No H-bonds generated for 'chain 'A' and resid 622 through 624' Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'B' and resid 23 through 27 removed outlier: 4.027A pdb=" N GLU B 26 " --> pdb=" O PHE B 23 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU B 27 " --> pdb=" O ASN B 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 23 through 27' Processing helix chain 'B' and resid 232 through 236 removed outlier: 4.301A pdb=" N ALA B 235 " --> pdb=" O ILE B 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 43 removed outlier: 3.633A pdb=" N LEU C 42 " --> pdb=" O GLU C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 66 removed outlier: 4.574A pdb=" N TYR C 65 " --> pdb=" O SER C 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 46 Processing helix chain 'D' and resid 47 through 62 Processing helix chain 'D' and resid 66 through 82 removed outlier: 4.483A pdb=" N GLN D 70 " --> pdb=" O PRO D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 104 through 119 Processing helix chain 'D' and resid 123 through 129 Processing helix chain 'D' and resid 136 through 154 removed outlier: 4.670A pdb=" N ALA D 140 " --> pdb=" O ASP D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 189 removed outlier: 3.593A pdb=" N TYR D 184 " --> pdb=" O SER D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 225 Proline residue: D 216 - end of helix removed outlier: 3.716A pdb=" N ASN D 220 " --> pdb=" O PRO D 216 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG D 223 " --> pdb=" O GLU D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 242 Processing helix chain 'E' and resid 39 through 46 removed outlier: 3.695A pdb=" N ILE E 46 " --> pdb=" O ASP E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 100 removed outlier: 7.214A pdb=" N LEU A 165 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE A 97 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU A 167 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N PHE A 99 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N PHE A 169 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 176 through 183 removed outlier: 6.525A pdb=" N ILE A 254 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN A 179 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ASN A 259 " --> pdb=" O SER A 242 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N SER A 242 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 276 removed outlier: 6.181A pdb=" N LYS A 267 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LEU A 337 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N SER A 269 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 12.700A pdb=" N VAL A 339 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 9.775A pdb=" N VAL A 271 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 12.216A pdb=" N VAL A 341 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 9.594A pdb=" N VAL A 273 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 355 removed outlier: 4.270A pdb=" N VAL A 349 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL A 414 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LYS A 351 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N TYR A 416 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ARG A 353 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N VAL A 418 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLU A 355 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N GLU A 420 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 427 through 433 removed outlier: 3.936A pdb=" N SER A 439 " --> pdb=" O GLY A 431 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TYR A 477 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL A 483 " --> pdb=" O TYR A 477 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ASN A 523 " --> pdb=" O ILE A 519 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 599 " --> pdb=" O PHE A 572 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY A 590 " --> pdb=" O TYR A 618 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL A 628 " --> pdb=" O ILE A 719 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TRP A 745 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE A 791 " --> pdb=" O MET A 768 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A 770 " --> pdb=" O GLN A 789 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR A 432 " --> pdb=" O PHE A 804 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ILE A 806 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ILE A 430 " --> pdb=" O ILE A 806 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 45 through 51 removed outlier: 6.685A pdb=" N SER B 389 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N SER B 49 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL B 387 " --> pdb=" O SER B 49 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 66 through 68 removed outlier: 3.602A pdb=" N ALA B 68 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL B 81 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N SER B 94 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ALA B 83 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 111 through 118 removed outlier: 6.472A pdb=" N GLY B 114 " --> pdb=" O GLY B 125 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLY B 125 " --> pdb=" O GLY B 114 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N GLN B 130 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL B 131 " --> pdb=" O GLN B 144 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLN B 144 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ALA B 133 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 156 through 158 removed outlier: 6.665A pdb=" N LEU B 171 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N THR B 184 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA B 173 " --> pdb=" O LYS B 182 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 201 through 203 removed outlier: 6.832A pdb=" N VAL B 216 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N GLN B 229 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ALA B 218 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 252 through 254 removed outlier: 3.551A pdb=" N THR B 268 " --> pdb=" O ALA B 260 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ALA B 269 " --> pdb=" O MET B 278 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 286 through 291 removed outlier: 4.191A pdb=" N ASP B 288 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TRP B 317 " --> pdb=" O ALA B 307 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N THR B 309 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR B 315 " --> pdb=" O THR B 309 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 331 through 333 removed outlier: 5.743A pdb=" N ASN B 350 " --> pdb=" O PHE B 356 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N PHE B 356 " --> pdb=" O ASN B 350 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 32 through 35 removed outlier: 3.806A pdb=" N ILE E 32 " --> pdb=" O GLN E 80 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 32 through 35 removed outlier: 3.806A pdb=" N ILE E 32 " --> pdb=" O GLN E 80 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR E 94 " --> pdb=" O ASN E 103 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASN E 103 " --> pdb=" O THR E 94 " (cutoff:3.500A) 507 hydrogen bonds defined for protein. 1422 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: 4.57 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 11051 1.04 - 1.23: 175 1.23 - 1.43: 4912 1.43 - 1.62: 6591 1.62 - 1.82: 61 Bond restraints: 22790 Sorted by residual: bond pdb=" N CYS C 25 " pdb=" H1 CYS C 25 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N VAL A 629 " pdb=" CA VAL A 629 " ideal model delta sigma weight residual 1.459 1.497 -0.037 1.19e-02 7.06e+03 9.84e+00 bond pdb=" N LEU A 630 " pdb=" CA LEU A 630 " ideal model delta sigma weight residual 1.456 1.493 -0.036 1.21e-02 6.83e+03 9.00e+00 bond pdb=" N GLU D 26 " pdb=" CA GLU D 26 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 bond pdb=" N LEU B 22 " pdb=" CA LEU B 22 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 ... (remaining 22785 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.91: 40822 3.91 - 7.83: 160 7.83 - 11.74: 4 11.74 - 15.66: 2 15.66 - 19.57: 2 Bond angle restraints: 40990 Sorted by residual: angle pdb=" N GLN A 446 " pdb=" CA GLN A 446 " pdb=" C GLN A 446 " ideal model delta sigma weight residual 110.80 130.37 -19.57 2.13e+00 2.20e-01 8.44e+01 angle pdb=" N GLN A 446 " pdb=" CA GLN A 446 " pdb=" HA GLN A 446 " ideal model delta sigma weight residual 110.00 92.13 17.87 3.00e+00 1.11e-01 3.55e+01 angle pdb=" C GLN A 446 " pdb=" N ASP A 447 " pdb=" CA ASP A 447 " ideal model delta sigma weight residual 122.42 113.66 8.76 1.55e+00 4.16e-01 3.19e+01 angle pdb=" N PRO E 108 " pdb=" CA PRO E 108 " pdb=" C PRO E 108 " ideal model delta sigma weight residual 112.47 101.75 10.72 2.06e+00 2.36e-01 2.71e+01 angle pdb=" CB GLN A 446 " pdb=" CA GLN A 446 " pdb=" HA GLN A 446 " ideal model delta sigma weight residual 109.00 124.36 -15.36 3.00e+00 1.11e-01 2.62e+01 ... (remaining 40985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 9806 17.72 - 35.45: 705 35.45 - 53.17: 240 53.17 - 70.90: 59 70.90 - 88.62: 18 Dihedral angle restraints: 10828 sinusoidal: 5824 harmonic: 5004 Sorted by residual: dihedral pdb=" CA TRP A 449 " pdb=" C TRP A 449 " pdb=" N LEU A 450 " pdb=" CA LEU A 450 " ideal model delta harmonic sigma weight residual 180.00 -152.66 -27.34 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA SER C 62 " pdb=" C SER C 62 " pdb=" N GLY C 63 " pdb=" CA GLY C 63 " ideal model delta harmonic sigma weight residual 180.00 153.68 26.32 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA LEU A 450 " pdb=" C LEU A 450 " pdb=" N GLY A 451 " pdb=" CA GLY A 451 " ideal model delta harmonic sigma weight residual 180.00 154.15 25.85 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 10825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 1723 0.134 - 0.268: 9 0.268 - 0.401: 0 0.401 - 0.535: 0 0.535 - 0.669: 1 Chirality restraints: 1733 Sorted by residual: chirality pdb=" CA GLN A 446 " pdb=" N GLN A 446 " pdb=" C GLN A 446 " pdb=" CB GLN A 446 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.12e+01 chirality pdb=" CA VAL A 629 " pdb=" N VAL A 629 " pdb=" C VAL A 629 " pdb=" CB VAL A 629 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA ILE B 290 " pdb=" N ILE B 290 " pdb=" C ILE B 290 " pdb=" CB ILE B 290 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.14e-01 ... (remaining 1730 not shown) Planarity restraints: 3508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 803 " -0.029 2.00e-02 2.50e+03 2.49e-02 9.27e+00 pdb=" CD GLN A 803 " 0.032 2.00e-02 2.50e+03 pdb=" OE1 GLN A 803 " 0.005 2.00e-02 2.50e+03 pdb=" NE2 GLN A 803 " 0.003 2.00e-02 2.50e+03 pdb="HE21 GLN A 803 " 0.024 2.00e-02 2.50e+03 pdb="HE22 GLN A 803 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 540 " 0.048 5.00e-02 4.00e+02 7.18e-02 8.25e+00 pdb=" N PRO A 541 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 541 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 541 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 368 " 0.027 2.00e-02 2.50e+03 2.33e-02 8.12e+00 pdb=" CD GLN B 368 " -0.030 2.00e-02 2.50e+03 pdb=" OE1 GLN B 368 " -0.004 2.00e-02 2.50e+03 pdb=" NE2 GLN B 368 " -0.003 2.00e-02 2.50e+03 pdb="HE21 GLN B 368 " -0.022 2.00e-02 2.50e+03 pdb="HE22 GLN B 368 " 0.033 2.00e-02 2.50e+03 ... (remaining 3505 not shown) Histogram of nonbonded interaction distances: 1.31 - 1.97: 308 1.97 - 2.63: 27822 2.63 - 3.28: 67891 3.28 - 3.94: 85025 3.94 - 4.60: 133219 Nonbonded interactions: 314265 Sorted by model distance: nonbonded pdb=" OE2 GLU D 199 " pdb=" HE ARG D 203 " model vdw 1.311 2.450 nonbonded pdb=" HD2 TYR A 432 " pdb=" HB3 PHE A 804 " model vdw 1.316 2.270 nonbonded pdb=" HH TYR A 608 " pdb=" OE1 GLU A 650 " model vdw 1.453 2.450 nonbonded pdb=" O SER B 285 " pdb=" H GLN B 301 " model vdw 1.453 2.450 nonbonded pdb=" OE1 GLN A 542 " pdb=" H ALA A 544 " model vdw 1.454 2.450 ... (remaining 314260 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.320 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: 0.140 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 18.890 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11739 Z= 0.149 Angle : 0.682 19.570 15963 Z= 0.381 Chirality : 0.047 0.669 1733 Planarity : 0.004 0.072 2106 Dihedral : 13.935 88.624 4248 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.16 % Allowed : 4.80 % Favored : 95.04 % 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: -0.38 (0.22), residues: 1460 helix: 1.04 (0.28), residues: 320 sheet: 0.21 (0.23), residues: 432 loop : -1.15 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 392 TYR 0.021 0.001 TYR C 31 PHE 0.024 0.002 PHE B 204 TRP 0.015 0.001 TRP A 449 HIS 0.003 0.001 HIS A 533 Details of bonding type rmsd covalent geometry : bond 0.00276 (11738) covalent geometry : angle 0.68097 (15961) SS BOND : bond 0.00833 ( 1) SS BOND : angle 2.88464 ( 2) hydrogen bonds : bond 0.20065 ( 504) hydrogen bonds : angle 8.66725 ( 1422) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 100 time to evaluate : 0.545 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 67 LEU cc_start: 0.7601 (tp) cc_final: 0.7143 (mt) outliers start: 2 outliers final: 1 residues processed: 101 average time/residue: 0.1920 time to fit residues: 29.1686 Evaluate side-chains 69 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 651 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 GLN B 302 ASN D 89 GLN D 116 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.063401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.050038 restraints weight = 189782.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.052172 restraints weight = 90060.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.053572 restraints weight = 57099.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.054470 restraints weight = 42728.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.055083 restraints weight = 35373.547| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 11739 Z= 0.310 Angle : 0.716 6.917 15963 Z= 0.398 Chirality : 0.046 0.176 1733 Planarity : 0.005 0.078 2106 Dihedral : 7.193 52.583 1617 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.30 % Allowed : 7.40 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.92 (0.21), residues: 1460 helix: 0.70 (0.27), residues: 327 sheet: -0.38 (0.24), residues: 427 loop : -1.37 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 215 TYR 0.023 0.002 TYR C 31 PHE 0.021 0.002 PHE A 718 TRP 0.015 0.002 TRP B 279 HIS 0.009 0.002 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00632 (11738) covalent geometry : angle 0.71583 (15961) SS BOND : bond 0.00539 ( 1) SS BOND : angle 1.06370 ( 2) hydrogen bonds : bond 0.05221 ( 504) hydrogen bonds : angle 7.07410 ( 1422) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.452 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 189 MET cc_start: 0.9106 (OUTLIER) cc_final: 0.7758 (ppp) REVERT: B 226 MET cc_start: 0.7971 (tpp) cc_final: 0.7430 (tmm) outliers start: 16 outliers final: 10 residues processed: 73 average time/residue: 0.2135 time to fit residues: 22.9552 Evaluate side-chains 68 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 651 ASN Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain E residue 43 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 115 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 78 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.3682 r_free = 0.3682 target = 0.062646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.050014 restraints weight = 185191.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.052112 restraints weight = 86465.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.053491 restraints weight = 53777.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.054367 restraints weight = 39590.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.054844 restraints weight = 32433.452| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 11739 Z= 0.279 Angle : 0.663 9.228 15963 Z= 0.366 Chirality : 0.044 0.167 1733 Planarity : 0.005 0.062 2106 Dihedral : 7.060 52.398 1617 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 1.63 % Allowed : 8.37 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -1.15 (0.21), residues: 1460 helix: 0.93 (0.27), residues: 326 sheet: -0.67 (0.24), residues: 421 loop : -1.63 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 160 TYR 0.022 0.002 TYR C 31 PHE 0.015 0.002 PHE D 128 TRP 0.018 0.002 TRP A 449 HIS 0.006 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00567 (11738) covalent geometry : angle 0.66174 (15961) SS BOND : bond 0.01560 ( 1) SS BOND : angle 4.29533 ( 2) hydrogen bonds : bond 0.04840 ( 504) hydrogen bonds : angle 6.75091 ( 1422) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.651 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 189 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.7700 (ppp) outliers start: 20 outliers final: 13 residues processed: 76 average time/residue: 0.2316 time to fit residues: 26.3306 Evaluate side-chains 72 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 651 ASN Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain E residue 43 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 143 optimal weight: 0.7980 chunk 141 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 8 optimal weight: 0.0270 chunk 110 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 142 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 137 optimal weight: 0.5980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.063780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.050850 restraints weight = 183973.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.053051 restraints weight = 84982.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.054470 restraints weight = 52889.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.055395 restraints weight = 38999.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.055981 restraints weight = 31843.779| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 11739 Z= 0.115 Angle : 0.566 5.992 15963 Z= 0.309 Chirality : 0.044 0.162 1733 Planarity : 0.004 0.051 2106 Dihedral : 6.597 49.915 1617 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.81 % Allowed : 9.02 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.79 (0.22), residues: 1460 helix: 1.53 (0.28), residues: 328 sheet: -0.66 (0.24), residues: 419 loop : -1.43 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 160 TYR 0.024 0.001 TYR C 31 PHE 0.016 0.001 PHE D 128 TRP 0.020 0.001 TRP B 317 HIS 0.002 0.001 HIS A 555 Details of bonding type rmsd covalent geometry : bond 0.00243 (11738) covalent geometry : angle 0.56466 (15961) SS BOND : bond 0.00046 ( 1) SS BOND : angle 4.02107 ( 2) hydrogen bonds : bond 0.03927 ( 504) hydrogen bonds : angle 6.20177 ( 1422) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.642 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 10 residues processed: 68 average time/residue: 0.2174 time to fit residues: 23.1371 Evaluate side-chains 67 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 651 ASN Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 87 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 40 optimal weight: 5.9990 chunk 98 optimal weight: 0.2980 chunk 117 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 110 optimal weight: 0.4980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 302 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.063931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.050985 restraints weight = 186633.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.053175 restraints weight = 87573.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.054594 restraints weight = 54997.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.055481 restraints weight = 40880.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.055978 restraints weight = 33743.360| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 11739 Z= 0.114 Angle : 0.536 6.349 15963 Z= 0.292 Chirality : 0.043 0.152 1733 Planarity : 0.004 0.049 2106 Dihedral : 6.204 45.373 1617 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.89 % Allowed : 9.76 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.68 (0.22), residues: 1460 helix: 1.76 (0.28), residues: 328 sheet: -0.67 (0.24), residues: 409 loop : -1.37 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 160 TYR 0.025 0.001 TYR C 31 PHE 0.016 0.001 PHE A 785 TRP 0.023 0.001 TRP B 317 HIS 0.002 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00244 (11738) covalent geometry : angle 0.53585 (15961) SS BOND : bond 0.00180 ( 1) SS BOND : angle 1.96021 ( 2) hydrogen bonds : bond 0.03672 ( 504) hydrogen bonds : angle 5.88236 ( 1422) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.616 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 68 average time/residue: 0.2059 time to fit residues: 21.8610 Evaluate side-chains 66 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain E residue 43 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 26 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 141 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 76 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 51 optimal weight: 0.0470 chunk 43 optimal weight: 0.5980 chunk 45 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 overall best weight: 1.6482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.063232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.050544 restraints weight = 185944.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.052716 restraints weight = 86295.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.054115 restraints weight = 53545.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.055029 restraints weight = 39388.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.055614 restraints weight = 32095.615| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 11739 Z= 0.161 Angle : 0.543 6.699 15963 Z= 0.296 Chirality : 0.042 0.180 1733 Planarity : 0.004 0.046 2106 Dihedral : 5.931 42.348 1615 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.68 % Favored : 94.25 % Rotamer: Outliers : 1.14 % Allowed : 9.76 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.72 (0.22), residues: 1460 helix: 1.75 (0.29), residues: 328 sheet: -0.79 (0.24), residues: 424 loop : -1.34 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 188 TYR 0.025 0.001 TYR C 31 PHE 0.015 0.001 PHE A 785 TRP 0.024 0.001 TRP B 317 HIS 0.004 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00334 (11738) covalent geometry : angle 0.54304 (15961) SS BOND : bond 0.00075 ( 1) SS BOND : angle 1.74636 ( 2) hydrogen bonds : bond 0.03656 ( 504) hydrogen bonds : angle 5.85257 ( 1422) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.624 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.9229 (OUTLIER) cc_final: 0.8602 (m-30) outliers start: 14 outliers final: 10 residues processed: 68 average time/residue: 0.1977 time to fit residues: 20.8573 Evaluate side-chains 66 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 766 ILE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain E residue 43 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 43 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 125 optimal weight: 9.9990 chunk 139 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.062509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.049597 restraints weight = 186345.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.051717 restraints weight = 87835.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.053104 restraints weight = 55039.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.054010 restraints weight = 40667.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.054590 restraints weight = 33275.148| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 11739 Z= 0.212 Angle : 0.566 7.088 15963 Z= 0.310 Chirality : 0.042 0.144 1733 Planarity : 0.004 0.046 2106 Dihedral : 5.956 38.627 1615 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.78 % Favored : 93.15 % Rotamer: Outliers : 1.54 % Allowed : 9.59 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.87 (0.22), residues: 1460 helix: 1.58 (0.28), residues: 328 sheet: -0.86 (0.24), residues: 411 loop : -1.42 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 188 TYR 0.026 0.002 TYR C 31 PHE 0.015 0.002 PHE A 785 TRP 0.015 0.001 TRP A 449 HIS 0.005 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00438 (11738) covalent geometry : angle 0.56577 (15961) SS BOND : bond 0.00018 ( 1) SS BOND : angle 1.50006 ( 2) hydrogen bonds : bond 0.03793 ( 504) hydrogen bonds : angle 5.92122 ( 1422) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 54 time to evaluate : 0.493 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 226 MET cc_start: 0.8248 (tpp) cc_final: 0.7769 (tmm) outliers start: 19 outliers final: 14 residues processed: 70 average time/residue: 0.1836 time to fit residues: 20.2872 Evaluate side-chains 68 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain E residue 43 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 115 optimal weight: 0.0470 chunk 144 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 82 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 109 optimal weight: 9.9990 overall best weight: 1.1284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN B 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.063342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.050541 restraints weight = 182377.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.052698 restraints weight = 85491.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.054098 restraints weight = 53048.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.055004 restraints weight = 38928.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.055604 restraints weight = 31841.382| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 11739 Z= 0.125 Angle : 0.527 6.810 15963 Z= 0.285 Chirality : 0.043 0.145 1733 Planarity : 0.004 0.045 2106 Dihedral : 5.729 37.436 1615 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.41 % Favored : 94.52 % Rotamer: Outliers : 0.98 % Allowed : 9.84 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 (0.22), residues: 1460 helix: 1.95 (0.29), residues: 322 sheet: -0.89 (0.24), residues: 422 loop : -1.30 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 188 TYR 0.024 0.001 TYR C 31 PHE 0.015 0.001 PHE A 785 TRP 0.018 0.001 TRP B 317 HIS 0.003 0.001 HIS A 555 Details of bonding type rmsd covalent geometry : bond 0.00261 (11738) covalent geometry : angle 0.52668 (15961) SS BOND : bond 0.00039 ( 1) SS BOND : angle 1.28594 ( 2) hydrogen bonds : bond 0.03507 ( 504) hydrogen bonds : angle 5.65375 ( 1422) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.650 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 11 residues processed: 65 average time/residue: 0.1928 time to fit residues: 19.4456 Evaluate side-chains 65 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain E residue 43 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 35 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 53 optimal weight: 0.1980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 GLN ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.062472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.049485 restraints weight = 184446.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.051618 restraints weight = 87264.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.053003 restraints weight = 54618.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.053900 restraints weight = 40453.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.054492 restraints weight = 33248.782| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 11739 Z= 0.196 Angle : 0.556 7.389 15963 Z= 0.303 Chirality : 0.042 0.144 1733 Planarity : 0.004 0.044 2106 Dihedral : 5.757 38.521 1615 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.33 % Favored : 92.60 % Rotamer: Outliers : 1.06 % Allowed : 10.08 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.84 (0.22), residues: 1460 helix: 1.79 (0.29), residues: 321 sheet: -1.03 (0.23), residues: 440 loop : -1.34 (0.24), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 391 TYR 0.022 0.002 TYR C 31 PHE 0.016 0.001 PHE A 785 TRP 0.018 0.001 TRP B 317 HIS 0.005 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00407 (11738) covalent geometry : angle 0.55581 (15961) SS BOND : bond 0.00011 ( 1) SS BOND : angle 1.19751 ( 2) hydrogen bonds : bond 0.03661 ( 504) hydrogen bonds : angle 5.76124 ( 1422) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.601 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 64 average time/residue: 0.1932 time to fit residues: 19.2884 Evaluate side-chains 62 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain E residue 43 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 56 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 142 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 136 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.062488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.049511 restraints weight = 185175.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.051644 restraints weight = 86950.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.053023 restraints weight = 54554.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.053936 restraints weight = 40355.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.054516 restraints weight = 33044.538| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 11739 Z= 0.181 Angle : 0.548 7.109 15963 Z= 0.298 Chirality : 0.042 0.157 1733 Planarity : 0.004 0.044 2106 Dihedral : 5.724 38.004 1615 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.71 % Favored : 93.22 % Rotamer: Outliers : 0.89 % Allowed : 10.41 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.82 (0.22), residues: 1460 helix: 1.78 (0.28), residues: 321 sheet: -1.04 (0.23), residues: 447 loop : -1.29 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 188 TYR 0.022 0.001 TYR C 31 PHE 0.015 0.001 PHE A 785 TRP 0.020 0.001 TRP B 317 HIS 0.004 0.001 HIS A 555 Details of bonding type rmsd covalent geometry : bond 0.00373 (11738) covalent geometry : angle 0.54810 (15961) SS BOND : bond 0.00055 ( 1) SS BOND : angle 1.11178 ( 2) hydrogen bonds : bond 0.03592 ( 504) hydrogen bonds : angle 5.68557 ( 1422) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.631 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 11 residues processed: 62 average time/residue: 0.1947 time to fit residues: 18.9535 Evaluate side-chains 63 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain E residue 43 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.062784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.049695 restraints weight = 186604.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.051855 restraints weight = 88227.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.053250 restraints weight = 55461.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.054163 restraints weight = 41221.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.054766 restraints weight = 33842.959| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 11739 Z= 0.156 Angle : 0.535 6.948 15963 Z= 0.290 Chirality : 0.042 0.143 1733 Planarity : 0.004 0.043 2106 Dihedral : 5.628 38.336 1615 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.85 % Favored : 93.08 % Rotamer: Outliers : 1.14 % Allowed : 10.41 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.78 (0.22), residues: 1460 helix: 1.87 (0.29), residues: 321 sheet: -1.07 (0.23), residues: 447 loop : -1.24 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 188 TYR 0.021 0.001 TYR C 31 PHE 0.015 0.001 PHE A 785 TRP 0.035 0.002 TRP B 317 HIS 0.003 0.001 HIS A 555 Details of bonding type rmsd covalent geometry : bond 0.00324 (11738) covalent geometry : angle 0.53483 (15961) SS BOND : bond 0.00015 ( 1) SS BOND : angle 1.04931 ( 2) hydrogen bonds : bond 0.03517 ( 504) hydrogen bonds : angle 5.62987 ( 1422) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3217.26 seconds wall clock time: 55 minutes 42.30 seconds (3342.30 seconds total)