Starting phenix.real_space_refine on Thu Mar 5 19:12:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i60_52644/03_2026/9i60_52644_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i60_52644/03_2026/9i60_52644.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9i60_52644/03_2026/9i60_52644_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i60_52644/03_2026/9i60_52644_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9i60_52644/03_2026/9i60_52644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i60_52644/03_2026/9i60_52644.map" } resolution = 3.31 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= 0.004 sd= 0.018 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 8 5.49 5 S 48 5.16 5 C 7869 2.51 5 N 1831 2.21 5 O 2085 1.98 5 H 11527 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 23368 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 7757 Classifications: {'peptide': 510} Link IDs: {'PTRANS': 13, 'TRANS': 496} Chain: "B" Number of atoms: 7595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 7595 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 13, 'TRANS': 487} Chain: "C" Number of atoms: 7612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 7612 Classifications: {'peptide': 502} Link IDs: {'PTRANS': 13, 'TRANS': 488} Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGT': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'PGT': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 251 Unusual residues: {'CDL': 2, 'PGT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.52, per 1000 atoms: 0.19 Number of scatterers: 23368 At special positions: 0 Unit cell: (81.2773, 115.998, 111.263, 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 48 16.00 P 8 15.00 O 2085 8.00 N 1831 7.00 C 7869 6.00 H 11527 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.09 Conformation dependent library (CDL) restraints added in 743.8 milliseconds 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2690 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 0 sheets defined 82.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 59 through 80 Proline residue: A 65 - end of helix Processing helix chain 'A' and resid 80 through 119 removed outlier: 5.822A pdb=" N TRP A 101 " --> pdb=" O ASP A 97 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ALA A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR A 108 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL A 111 " --> pdb=" O GLY A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 148 removed outlier: 3.519A pdb=" N ALA A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA A 148 " --> pdb=" O MET A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 169 removed outlier: 3.881A pdb=" N PHE A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N THR A 159 " --> pdb=" O MET A 155 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N THR A 160 " --> pdb=" O PHE A 156 " (cutoff:3.500A) Proline residue: A 162 - end of helix Processing helix chain 'A' and resid 177 through 188 removed outlier: 3.654A pdb=" N HIS A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 210 Processing helix chain 'A' and resid 216 through 221 removed outlier: 3.681A pdb=" N ALA A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 216 through 221' Processing helix chain 'A' and resid 221 through 230 removed outlier: 6.584A pdb=" N GLU A 227 " --> pdb=" O PRO A 223 " (cutoff:3.500A) removed outlier: 9.032A pdb=" N LYS A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 268 removed outlier: 3.582A pdb=" N ASP A 239 " --> pdb=" O GLY A 235 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ILE A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 266 " --> pdb=" O GLY A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 296 removed outlier: 3.526A pdb=" N SER A 296 " --> pdb=" O PHE A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 324 removed outlier: 3.526A pdb=" N GLN A 303 " --> pdb=" O GLY A 299 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 343 removed outlier: 3.762A pdb=" N LEU A 333 " --> pdb=" O ILE A 329 " (cutoff:3.500A) Proline residue: A 334 - end of helix Processing helix chain 'A' and resid 343 through 349 Processing helix chain 'A' and resid 360 through 366 removed outlier: 3.848A pdb=" N SER A 365 " --> pdb=" O GLU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 389 Proline residue: A 379 - end of helix removed outlier: 4.060A pdb=" N ILE A 388 " --> pdb=" O PHE A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 426 Proline residue: A 405 - end of helix removed outlier: 4.263A pdb=" N THR A 419 " --> pdb=" O ILE A 415 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 420 " --> pdb=" O PHE A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 446 Processing helix chain 'A' and resid 449 through 481 removed outlier: 4.154A pdb=" N MET A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 475 " --> pdb=" O SER A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 509 removed outlier: 3.516A pdb=" N GLY A 496 " --> pdb=" O THR A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 527 Processing helix chain 'A' and resid 528 through 546 removed outlier: 3.989A pdb=" N VAL A 532 " --> pdb=" O PRO A 528 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE A 538 " --> pdb=" O ILE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 565 Processing helix chain 'B' and resid 59 through 80 Proline residue: B 65 - end of helix Processing helix chain 'B' and resid 80 through 119 removed outlier: 5.484A pdb=" N TRP B 101 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ALA B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR B 108 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL B 111 " --> pdb=" O GLY B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 125 removed outlier: 3.618A pdb=" N THR B 124 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 159 through 168 removed outlier: 3.840A pdb=" N LEU B 163 " --> pdb=" O THR B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 188 removed outlier: 3.848A pdb=" N MET B 186 " --> pdb=" O MET B 182 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N HIS B 188 " --> pdb=" O THR B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 209 Processing helix chain 'B' and resid 217 through 220 Processing helix chain 'B' and resid 221 through 233 removed outlier: 7.003A pdb=" N GLU B 227 " --> pdb=" O PRO B 223 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N LYS B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY B 229 " --> pdb=" O ILE B 225 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU B 231 " --> pdb=" O GLU B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 268 removed outlier: 3.660A pdb=" N THR B 250 " --> pdb=" O THR B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 295 Processing helix chain 'B' and resid 300 through 323 removed outlier: 3.689A pdb=" N TYR B 304 " --> pdb=" O LYS B 300 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B 305 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET B 310 " --> pdb=" O SER B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 331 Processing helix chain 'B' and resid 331 through 348 removed outlier: 3.713A pdb=" N GLY B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N PHE B 345 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN B 346 " --> pdb=" O SER B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 389 Proline residue: B 379 - end of helix removed outlier: 3.844A pdb=" N ARG B 387 " --> pdb=" O MET B 383 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE B 388 " --> pdb=" O PHE B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 426 Proline residue: B 405 - end of helix removed outlier: 4.190A pdb=" N THR B 419 " --> pdb=" O ILE B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 437 No H-bonds generated for 'chain 'B' and resid 435 through 437' Processing helix chain 'B' and resid 438 through 447 Processing helix chain 'B' and resid 450 through 480 removed outlier: 3.779A pdb=" N ILE B 455 " --> pdb=" O GLN B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 509 removed outlier: 3.560A pdb=" N LEU B 507 " --> pdb=" O GLY B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 546 removed outlier: 3.880A pdb=" N THR B 522 " --> pdb=" O LEU B 518 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR B 527 " --> pdb=" O ILE B 523 " (cutoff:3.500A) Proline residue: B 528 - end of helix removed outlier: 4.195A pdb=" N PHE B 531 " --> pdb=" O THR B 527 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL B 532 " --> pdb=" O PRO B 528 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE B 538 " --> pdb=" O ILE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 556 removed outlier: 3.654A pdb=" N GLN B 556 " --> pdb=" O GLU B 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 80 Proline residue: C 65 - end of helix Processing helix chain 'C' and resid 80 through 120 removed outlier: 5.855A pdb=" N TRP C 101 " --> pdb=" O ASP C 97 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ALA C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N THR C 108 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL C 111 " --> pdb=" O GLY C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 125 removed outlier: 3.843A pdb=" N THR C 124 " --> pdb=" O LYS C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 147 Processing helix chain 'C' and resid 152 through 157 Processing helix chain 'C' and resid 159 through 168 removed outlier: 3.675A pdb=" N LEU C 163 " --> pdb=" O THR C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 190 removed outlier: 3.626A pdb=" N HIS C 188 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP C 189 " --> pdb=" O THR C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 209 Processing helix chain 'C' and resid 216 through 221 removed outlier: 3.853A pdb=" N ALA C 220 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 216 through 221' Processing helix chain 'C' and resid 221 through 231 removed outlier: 7.270A pdb=" N GLU C 227 " --> pdb=" O PRO C 223 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N LYS C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU C 231 " --> pdb=" O GLU C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 268 Processing helix chain 'C' and resid 277 through 295 Processing helix chain 'C' and resid 303 through 324 Processing helix chain 'C' and resid 327 through 344 Proline residue: C 334 - end of helix Processing helix chain 'C' and resid 362 through 367 Processing helix chain 'C' and resid 367 through 389 Proline residue: C 379 - end of helix removed outlier: 3.668A pdb=" N ARG C 387 " --> pdb=" O MET C 383 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE C 388 " --> pdb=" O PHE C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 427 Proline residue: C 405 - end of helix removed outlier: 4.121A pdb=" N THR C 419 " --> pdb=" O ILE C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 437 No H-bonds generated for 'chain 'C' and resid 435 through 437' Processing helix chain 'C' and resid 438 through 446 Processing helix chain 'C' and resid 449 through 480 removed outlier: 4.050A pdb=" N MET C 453 " --> pdb=" O GLY C 449 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE C 455 " --> pdb=" O GLN C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 509 removed outlier: 3.934A pdb=" N LEU C 507 " --> pdb=" O GLY C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 546 removed outlier: 3.523A pdb=" N ILE C 523 " --> pdb=" O GLN C 519 " (cutoff:3.500A) Proline residue: C 528 - end of helix removed outlier: 4.411A pdb=" N PHE C 531 " --> pdb=" O THR C 527 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL C 532 " --> pdb=" O PRO C 528 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE C 538 " --> pdb=" O ILE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 557 855 hydrogen bonds defined for protein. 2553 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: 5.46 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11524 1.03 - 1.23: 19 1.23 - 1.42: 5057 1.42 - 1.61: 6959 1.61 - 1.81: 101 Bond restraints: 23660 Sorted by residual: bond pdb=" CE1 PHE A 464 " pdb=" CZ PHE A 464 " ideal model delta sigma weight residual 1.382 1.327 0.055 3.00e-02 1.11e+03 3.35e+00 bond pdb=" N ALA C 56 " pdb=" CA ALA C 56 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.31e+00 bond pdb=" N ALA B 56 " pdb=" CA ALA B 56 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" N ALA A 56 " pdb=" CA ALA A 56 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.81e+00 bond pdb=" CG1 ILE C 114 " pdb=" CD1 ILE C 114 " ideal model delta sigma weight residual 1.513 1.448 0.065 3.90e-02 6.57e+02 2.78e+00 ... (remaining 23655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 40933 1.49 - 2.99: 1375 2.99 - 4.48: 101 4.48 - 5.98: 29 5.98 - 7.47: 8 Bond angle restraints: 42446 Sorted by residual: angle pdb=" N VAL B 247 " pdb=" CA VAL B 247 " pdb=" C VAL B 247 " ideal model delta sigma weight residual 111.58 108.12 3.46 1.06e+00 8.90e-01 1.07e+01 angle pdb=" N ALA A 148 " pdb=" CA ALA A 148 " pdb=" CB ALA A 148 " ideal model delta sigma weight residual 113.65 109.73 3.92 1.47e+00 4.63e-01 7.12e+00 angle pdb=" CA6 CDL C 603 " pdb=" CA4 CDL C 603 " pdb=" OA6 CDL C 603 " ideal model delta sigma weight residual 107.81 101.37 6.44 2.43e+00 1.69e-01 7.02e+00 angle pdb=" C GLU C 272 " pdb=" N ASP C 273 " pdb=" CA ASP C 273 " ideal model delta sigma weight residual 121.80 128.07 -6.27 2.44e+00 1.68e-01 6.61e+00 angle pdb=" CA3 CDL C 601 " pdb=" CA4 CDL C 601 " pdb=" OA6 CDL C 601 " ideal model delta sigma weight residual 107.81 101.76 6.05 2.43e+00 1.69e-01 6.21e+00 ... (remaining 42441 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.17: 10703 29.17 - 58.33: 562 58.33 - 87.50: 29 87.50 - 116.66: 3 116.66 - 145.83: 1 Dihedral angle restraints: 11298 sinusoidal: 6040 harmonic: 5258 Sorted by residual: dihedral pdb=" C3 PGT B 602 " pdb=" C1 PGT B 602 " pdb=" C2 PGT B 602 " pdb=" O3P PGT B 602 " ideal model delta sinusoidal sigma weight residual 293.87 148.04 145.83 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" CA5 CDL C 601 " pdb=" CA4 CDL C 601 " pdb=" OA6 CDL C 601 " pdb=" CA6 CDL C 601 " ideal model delta sinusoidal sigma weight residual 168.24 51.94 116.30 1 3.00e+01 1.11e-03 1.54e+01 dihedral pdb=" CA PRO C 134 " pdb=" C PRO C 134 " pdb=" N GLU C 135 " pdb=" CA GLU C 135 " ideal model delta harmonic sigma weight residual -180.00 -161.41 -18.59 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 11295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1716 0.069 - 0.137: 161 0.137 - 0.206: 2 0.206 - 0.274: 0 0.274 - 0.343: 4 Chirality restraints: 1883 Sorted by residual: chirality pdb=" CA4 CDL C 603 " pdb=" CA3 CDL C 603 " pdb=" CA6 CDL C 603 " pdb=" OA6 CDL C 603 " both_signs ideal model delta sigma weight residual False -2.57 -2.92 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CA4 CDL C 601 " pdb=" CA3 CDL C 601 " pdb=" CA6 CDL C 601 " pdb=" OA6 CDL C 601 " both_signs ideal model delta sigma weight residual False -2.57 -2.90 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CB4 CDL C 603 " pdb=" CB3 CDL C 603 " pdb=" CB6 CDL C 603 " pdb=" OB6 CDL C 603 " both_signs ideal model delta sigma weight residual False -2.57 -2.89 0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 1880 not shown) Planarity restraints: 3457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 464 " 0.031 2.00e-02 2.50e+03 2.27e-02 1.55e+01 pdb=" CG PHE A 464 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 PHE A 464 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE A 464 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A 464 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 464 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 464 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE A 464 " -0.013 2.00e-02 2.50e+03 pdb=" HD2 PHE A 464 " 0.003 2.00e-02 2.50e+03 pdb=" HE1 PHE A 464 " 0.010 2.00e-02 2.50e+03 pdb=" HE2 PHE A 464 " 0.009 2.00e-02 2.50e+03 pdb=" HZ PHE A 464 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 414 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.23e+00 pdb=" C SER B 414 " 0.036 2.00e-02 2.50e+03 pdb=" O SER B 414 " -0.013 2.00e-02 2.50e+03 pdb=" N ILE B 415 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 414 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.83e+00 pdb=" C SER A 414 " 0.034 2.00e-02 2.50e+03 pdb=" O SER A 414 " -0.013 2.00e-02 2.50e+03 pdb=" N ILE A 415 " -0.011 2.00e-02 2.50e+03 ... (remaining 3454 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 3049 2.27 - 2.85: 52003 2.85 - 3.44: 63590 3.44 - 4.02: 85165 4.02 - 4.60: 132824 Nonbonded interactions: 336631 Sorted by model distance: nonbonded pdb=" O SER B 275 " pdb=" HG1 THR B 278 " model vdw 1.691 2.450 nonbonded pdb=" O LEU A 332 " pdb=" H SER A 336 " model vdw 1.698 2.450 nonbonded pdb="HH12 ARG B 210 " pdb=" OD2 ASP B 547 " model vdw 1.724 2.450 nonbonded pdb=" OD1 ASP A 82 " pdb=" H SER A 83 " model vdw 1.735 2.450 nonbonded pdb=" O ILE A 63 " pdb=" H LEU A 67 " model vdw 1.736 2.450 ... (remaining 336626 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 56 through 556) selection = (chain 'B' and resid 56 through 556) selection = (chain 'C' and resid 56 through 556) } 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: 2.220 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: 0.130 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.970 Find NCS groups from input model: 0.380 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 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 : 0.004 0.065 12133 Z= 0.193 Angle : 0.642 7.474 16455 Z= 0.352 Chirality : 0.042 0.343 1883 Planarity : 0.004 0.046 1986 Dihedral : 14.848 145.829 4254 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: 0.85 (0.21), residues: 1507 helix: 1.02 (0.15), residues: 1152 sheet: None (None), residues: 0 loop : -0.74 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 350 TYR 0.010 0.001 TYR A 197 PHE 0.064 0.002 PHE A 464 TRP 0.019 0.001 TRP A 377 HIS 0.005 0.001 HIS A 445 Details of bonding type rmsd covalent geometry : bond 0.00440 (12133) covalent geometry : angle 0.64206 (16455) hydrogen bonds : bond 0.13496 ( 855) hydrogen bonds : angle 6.46616 ( 2553) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.2791 time to fit residues: 26.6107 Evaluate side-chains 54 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.3279 r_free = 0.3279 target = 0.061741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.050347 restraints weight = 139694.381| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 3.14 r_work: 0.2795 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12133 Z= 0.173 Angle : 0.510 6.010 16455 Z= 0.291 Chirality : 0.036 0.128 1883 Planarity : 0.004 0.042 1986 Dihedral : 12.268 134.040 1956 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.43 % Allowed : 2.64 % Favored : 96.94 % 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: 1.63 (0.22), residues: 1507 helix: 1.58 (0.15), residues: 1165 sheet: None (None), residues: 0 loop : -0.51 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 387 TYR 0.006 0.001 TYR C 340 PHE 0.017 0.001 PHE A 464 TRP 0.013 0.001 TRP B 194 HIS 0.003 0.001 HIS C 192 Details of bonding type rmsd covalent geometry : bond 0.00346 (12133) covalent geometry : angle 0.50993 (16455) hydrogen bonds : bond 0.05149 ( 855) hydrogen bonds : angle 4.90190 ( 2553) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.595 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: C 476 MET cc_start: 0.9333 (mtm) cc_final: 0.9111 (mtm) outliers start: 5 outliers final: 2 residues processed: 56 average time/residue: 0.2131 time to fit residues: 19.0789 Evaluate side-chains 55 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain B residue 377 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 52 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN B 176 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.060116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.048514 restraints weight = 141516.404| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 3.13 r_work: 0.2754 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 12133 Z= 0.218 Angle : 0.510 5.808 16455 Z= 0.292 Chirality : 0.037 0.129 1883 Planarity : 0.004 0.042 1986 Dihedral : 11.233 122.717 1956 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.34 % Allowed : 3.57 % Favored : 96.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.02 (0.22), residues: 1507 helix: 1.88 (0.15), residues: 1166 sheet: None (None), residues: 0 loop : -0.50 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 213 TYR 0.007 0.001 TYR C 206 PHE 0.013 0.001 PHE A 464 TRP 0.013 0.001 TRP B 194 HIS 0.005 0.001 HIS C 192 Details of bonding type rmsd covalent geometry : bond 0.00451 (12133) covalent geometry : angle 0.50962 (16455) hydrogen bonds : bond 0.04814 ( 855) hydrogen bonds : angle 4.56608 ( 2553) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.8984 (tmm) cc_final: 0.8593 (tmm) REVERT: C 476 MET cc_start: 0.9353 (mtm) cc_final: 0.9016 (mtm) outliers start: 4 outliers final: 3 residues processed: 56 average time/residue: 0.2050 time to fit residues: 18.3725 Evaluate side-chains 54 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain B residue 377 TRP Chi-restraints excluded: chain C residue 168 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 110 optimal weight: 8.9990 chunk 121 optimal weight: 4.9990 chunk 150 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 445 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.058746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.047243 restraints weight = 142870.564| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 3.09 r_work: 0.2717 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12133 Z= 0.257 Angle : 0.533 5.682 16455 Z= 0.307 Chirality : 0.037 0.123 1883 Planarity : 0.004 0.044 1986 Dihedral : 10.933 119.919 1956 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.26 % Allowed : 4.51 % Favored : 95.23 % 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: 2.10 (0.22), residues: 1507 helix: 1.96 (0.15), residues: 1167 sheet: None (None), residues: 0 loop : -0.55 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 213 TYR 0.008 0.001 TYR A 157 PHE 0.013 0.001 PHE C 146 TRP 0.014 0.001 TRP B 194 HIS 0.005 0.001 HIS C 192 Details of bonding type rmsd covalent geometry : bond 0.00531 (12133) covalent geometry : angle 0.53337 (16455) hydrogen bonds : bond 0.04738 ( 855) hydrogen bonds : angle 4.50091 ( 2553) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.9080 (tmm) cc_final: 0.8694 (tmm) REVERT: B 144 MET cc_start: 0.9133 (mtm) cc_final: 0.8880 (mtt) REVERT: C 476 MET cc_start: 0.9354 (mtm) cc_final: 0.8992 (mtm) outliers start: 3 outliers final: 3 residues processed: 54 average time/residue: 0.2141 time to fit residues: 18.4865 Evaluate side-chains 54 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain B residue 377 TRP Chi-restraints excluded: chain C residue 168 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 85 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 100 optimal weight: 8.9990 chunk 124 optimal weight: 6.9990 chunk 121 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 517 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.059169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.047546 restraints weight = 142324.326| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 3.15 r_work: 0.2727 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12133 Z= 0.198 Angle : 0.484 5.636 16455 Z= 0.275 Chirality : 0.036 0.124 1883 Planarity : 0.003 0.042 1986 Dihedral : 10.491 119.865 1956 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.43 % Allowed : 4.85 % Favored : 94.72 % 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: 2.34 (0.22), residues: 1507 helix: 2.12 (0.15), residues: 1171 sheet: None (None), residues: 0 loop : -0.48 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 392 TYR 0.006 0.001 TYR C 206 PHE 0.012 0.001 PHE C 146 TRP 0.013 0.001 TRP B 194 HIS 0.004 0.001 HIS C 192 Details of bonding type rmsd covalent geometry : bond 0.00409 (12133) covalent geometry : angle 0.48436 (16455) hydrogen bonds : bond 0.04435 ( 855) hydrogen bonds : angle 4.31971 ( 2553) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.9062 (tmm) cc_final: 0.8669 (tmm) REVERT: B 144 MET cc_start: 0.9027 (mtm) cc_final: 0.8409 (mtt) REVERT: C 476 MET cc_start: 0.9337 (mtm) cc_final: 0.8956 (mtm) outliers start: 5 outliers final: 3 residues processed: 54 average time/residue: 0.2235 time to fit residues: 19.2518 Evaluate side-chains 54 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain B residue 377 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 88 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 343 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.059390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.047878 restraints weight = 142312.307| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 3.15 r_work: 0.2737 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12133 Z= 0.168 Angle : 0.465 5.584 16455 Z= 0.264 Chirality : 0.035 0.125 1883 Planarity : 0.003 0.040 1986 Dihedral : 10.208 119.393 1956 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.26 % Allowed : 5.53 % Favored : 94.21 % 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: 2.52 (0.22), residues: 1507 helix: 2.26 (0.15), residues: 1170 sheet: None (None), residues: 0 loop : -0.45 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 392 TYR 0.006 0.001 TYR C 206 PHE 0.010 0.001 PHE C 146 TRP 0.013 0.001 TRP B 194 HIS 0.004 0.001 HIS C 192 Details of bonding type rmsd covalent geometry : bond 0.00346 (12133) covalent geometry : angle 0.46477 (16455) hydrogen bonds : bond 0.04256 ( 855) hydrogen bonds : angle 4.19554 ( 2553) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 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: A 310 MET cc_start: 0.9078 (tmm) cc_final: 0.8702 (tmm) REVERT: B 144 MET cc_start: 0.9069 (mtm) cc_final: 0.8596 (mtt) REVERT: C 476 MET cc_start: 0.9340 (mtm) cc_final: 0.8953 (mtm) outliers start: 3 outliers final: 3 residues processed: 54 average time/residue: 0.2124 time to fit residues: 18.2684 Evaluate side-chains 54 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain B residue 377 TRP Chi-restraints excluded: chain C residue 168 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 35 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 75 optimal weight: 0.0170 chunk 2 optimal weight: 0.8980 chunk 50 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 148 optimal weight: 0.9990 chunk 124 optimal weight: 7.9990 chunk 144 optimal weight: 9.9990 overall best weight: 1.9824 ------------------------------------------------------------------------------- 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 = 0.3249 r_free = 0.3249 target = 0.059874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.048406 restraints weight = 141122.116| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 3.15 r_work: 0.2751 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12133 Z= 0.140 Angle : 0.447 5.569 16455 Z= 0.252 Chirality : 0.035 0.124 1883 Planarity : 0.003 0.038 1986 Dihedral : 9.924 117.974 1956 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.26 % Allowed : 5.62 % Favored : 94.13 % 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: 2.68 (0.22), residues: 1507 helix: 2.37 (0.15), residues: 1171 sheet: None (None), residues: 0 loop : -0.39 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 392 TYR 0.005 0.001 TYR C 206 PHE 0.011 0.001 PHE C 146 TRP 0.012 0.001 TRP B 194 HIS 0.002 0.000 HIS C 192 Details of bonding type rmsd covalent geometry : bond 0.00287 (12133) covalent geometry : angle 0.44738 (16455) hydrogen bonds : bond 0.04097 ( 855) hydrogen bonds : angle 4.09674 ( 2553) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.9083 (tmm) cc_final: 0.8700 (tmm) REVERT: B 144 MET cc_start: 0.9033 (mtm) cc_final: 0.8398 (mtt) REVERT: C 476 MET cc_start: 0.9355 (mtm) cc_final: 0.8948 (mtm) outliers start: 3 outliers final: 2 residues processed: 55 average time/residue: 0.2109 time to fit residues: 18.4700 Evaluate side-chains 53 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain B residue 377 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 46 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 94 optimal weight: 0.0970 chunk 25 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- 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 = 0.3245 r_free = 0.3245 target = 0.059626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.048389 restraints weight = 140503.998| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 3.11 r_work: 0.2752 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12133 Z= 0.150 Angle : 0.452 5.559 16455 Z= 0.255 Chirality : 0.035 0.123 1883 Planarity : 0.003 0.039 1986 Dihedral : 9.739 117.779 1956 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.17 % Allowed : 6.04 % Favored : 93.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.78 (0.22), residues: 1507 helix: 2.44 (0.15), residues: 1171 sheet: None (None), residues: 0 loop : -0.36 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 213 TYR 0.005 0.001 TYR C 206 PHE 0.011 0.001 PHE C 146 TRP 0.012 0.001 TRP B 194 HIS 0.003 0.001 HIS C 192 Details of bonding type rmsd covalent geometry : bond 0.00309 (12133) covalent geometry : angle 0.45214 (16455) hydrogen bonds : bond 0.04049 ( 855) hydrogen bonds : angle 4.06002 ( 2553) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.9109 (tmm) cc_final: 0.8720 (tmm) REVERT: B 144 MET cc_start: 0.9040 (mtm) cc_final: 0.8400 (mtt) REVERT: C 476 MET cc_start: 0.9348 (mtm) cc_final: 0.8935 (mtm) outliers start: 2 outliers final: 2 residues processed: 53 average time/residue: 0.2065 time to fit residues: 17.5251 Evaluate side-chains 53 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain B residue 377 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 112 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 121 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3227 r_free = 0.3227 target = 0.058861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.047303 restraints weight = 142885.714| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 3.16 r_work: 0.2721 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 12133 Z= 0.219 Angle : 0.496 6.494 16455 Z= 0.282 Chirality : 0.036 0.121 1883 Planarity : 0.003 0.040 1986 Dihedral : 9.826 119.119 1956 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.17 % Allowed : 6.04 % Favored : 93.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.68 (0.22), residues: 1507 helix: 2.37 (0.15), residues: 1171 sheet: None (None), residues: 0 loop : -0.41 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 213 TYR 0.007 0.001 TYR C 206 PHE 0.012 0.001 PHE C 146 TRP 0.013 0.001 TRP C 194 HIS 0.004 0.001 HIS C 192 Details of bonding type rmsd covalent geometry : bond 0.00458 (12133) covalent geometry : angle 0.49617 (16455) hydrogen bonds : bond 0.04224 ( 855) hydrogen bonds : angle 4.16447 ( 2553) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.9121 (tmm) cc_final: 0.8743 (tmm) REVERT: B 144 MET cc_start: 0.9024 (mtm) cc_final: 0.8390 (mtt) REVERT: C 476 MET cc_start: 0.9357 (mtm) cc_final: 0.8947 (mtm) outliers start: 2 outliers final: 2 residues processed: 53 average time/residue: 0.2087 time to fit residues: 17.6498 Evaluate side-chains 53 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain B residue 377 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 119 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 80 optimal weight: 0.5980 chunk 71 optimal weight: 7.9990 chunk 87 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3280 r_free = 0.3280 target = 0.059971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.048323 restraints weight = 141055.731| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 3.09 r_work: 0.2773 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12133 Z= 0.115 Angle : 0.438 6.288 16455 Z= 0.243 Chirality : 0.035 0.126 1883 Planarity : 0.003 0.037 1986 Dihedral : 9.553 117.460 1956 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.26 % Allowed : 5.96 % Favored : 93.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.88 (0.22), residues: 1507 helix: 2.52 (0.15), residues: 1171 sheet: None (None), residues: 0 loop : -0.35 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 392 TYR 0.005 0.001 TYR A 197 PHE 0.009 0.001 PHE C 146 TRP 0.013 0.001 TRP A 377 HIS 0.002 0.000 HIS C 192 Details of bonding type rmsd covalent geometry : bond 0.00231 (12133) covalent geometry : angle 0.43813 (16455) hydrogen bonds : bond 0.03940 ( 855) hydrogen bonds : angle 3.97530 ( 2553) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3014 Ramachandran restraints generated. 1507 Oldfield, 0 Emsley, 1507 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 MET cc_start: 0.9087 (tmm) cc_final: 0.8699 (tmm) REVERT: B 144 MET cc_start: 0.9015 (mtm) cc_final: 0.8374 (mtt) outliers start: 3 outliers final: 2 residues processed: 55 average time/residue: 0.2108 time to fit residues: 18.7856 Evaluate side-chains 53 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain B residue 377 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 146 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 34 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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 = 0.3268 r_free = 0.3268 target = 0.059458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.047831 restraints weight = 141549.154| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 3.06 r_work: 0.2762 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12133 Z= 0.162 Angle : 0.455 5.568 16455 Z= 0.257 Chirality : 0.035 0.126 1883 Planarity : 0.003 0.039 1986 Dihedral : 9.520 117.277 1956 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.26 % Allowed : 6.13 % Favored : 93.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.89 (0.22), residues: 1507 helix: 2.53 (0.15), residues: 1171 sheet: None (None), residues: 0 loop : -0.34 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 213 TYR 0.006 0.001 TYR C 206 PHE 0.012 0.001 PHE C 146 TRP 0.012 0.001 TRP B 194 HIS 0.003 0.000 HIS C 192 Details of bonding type rmsd covalent geometry : bond 0.00334 (12133) covalent geometry : angle 0.45549 (16455) hydrogen bonds : bond 0.03979 ( 855) hydrogen bonds : angle 4.01747 ( 2553) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4222.08 seconds wall clock time: 72 minutes 35.36 seconds (4355.36 seconds total)