Starting phenix.real_space_refine on Fri Jul 3 05:45:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zrd_14911/07_2026/7zrd_14911.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zrd_14911/07_2026/7zrd_14911.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zrd_14911/07_2026/7zrd_14911.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zrd_14911/07_2026/7zrd_14911.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7zrd_14911/07_2026/7zrd_14911.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zrd_14911/07_2026/7zrd_14911.cif" model { file = "/net/cci-nas-00/data/ceres_data/7zrd_14911/07_2026/7zrd_14911.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zrd_14911/07_2026/7zrd_14911.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1080 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians K 9 8.98 5 V 1 8.30 5 P 5 5.49 5 S 62 5.16 5 C 7135 2.51 5 N 1823 2.21 5 O 2002 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11037 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4155 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain: "C" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1431 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 13, 'TRANS': 176} Chain: "D" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 216 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "B" Number of atoms: 5021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5021 Classifications: {'peptide': 676} Link IDs: {'PTRANS': 26, 'TRANS': 649} Chain: "A" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 207 Unusual residues: {' K': 7, 'CDL': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 7 Unusual residues: {' K': 2, 'VO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.61, per 1000 atoms: 0.24 Number of scatterers: 11037 At special positions: 0 Unit cell: (88.044, 112.332, 142.692, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) V 1 22.97 K 9 19.00 S 62 16.00 P 5 15.00 O 2002 8.00 N 1823 7.00 C 7135 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 617.5 milliseconds 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2642 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 9 sheets defined 62.8% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 1 through 32 Proline residue: A 22 - end of helix Processing helix chain 'A' and resid 41 through 51 Processing helix chain 'A' and resid 58 through 83 Processing helix chain 'A' and resid 84 through 87 removed outlier: 3.713A pdb=" N LEU A 87 " --> pdb=" O GLN A 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 84 through 87' Processing helix chain 'A' and resid 98 through 111 Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'A' and resid 125 through 132 Processing helix chain 'A' and resid 132 through 157 removed outlier: 3.662A pdb=" N ALA A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 177 Processing helix chain 'A' and resid 177 through 192 removed outlier: 3.643A pdb=" N VAL A 181 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 229 removed outlier: 4.120A pdb=" N GLN A 222 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 274 removed outlier: 4.398A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Proline residue: A 263 - end of helix Processing helix chain 'A' and resid 276 through 304 removed outlier: 4.019A pdb=" N GLY A 280 " --> pdb=" O ASP A 276 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.151A pdb=" N ALA A 311 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 342 Processing helix chain 'A' and resid 350 through 354 Processing helix chain 'A' and resid 355 through 368 removed outlier: 3.704A pdb=" N VAL A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 379 through 399 Processing helix chain 'A' and resid 410 through 437 removed outlier: 4.633A pdb=" N THR A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 449 through 465 removed outlier: 4.118A pdb=" N PHE A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 495 Processing helix chain 'A' and resid 496 through 508 Processing helix chain 'A' and resid 523 through 550 removed outlier: 4.037A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) Proline residue: A 545 - end of helix Processing helix chain 'A' and resid 550 through 557 Processing helix chain 'C' and resid 3 through 21 Processing helix chain 'C' and resid 21 through 34 Processing helix chain 'C' and resid 91 through 109 removed outlier: 3.649A pdb=" N ASP C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 140 removed outlier: 4.054A pdb=" N GLN C 140 " --> pdb=" O ALA C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 149 removed outlier: 3.627A pdb=" N VAL C 144 " --> pdb=" O GLN C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 162 Processing helix chain 'C' and resid 178 through 188 Processing helix chain 'D' and resid 2 through 25 Processing helix chain 'B' and resid 11 through 20 removed outlier: 4.000A pdb=" N GLN B 16 " --> pdb=" O THR B 12 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ALA B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 56 Processing helix chain 'B' and resid 63 through 102 removed outlier: 3.609A pdb=" N GLU B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLN B 93 " --> pdb=" O ARG B 89 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ALA B 94 " --> pdb=" O SER B 90 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL B 100 " --> pdb=" O SER B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 170 through 174 removed outlier: 3.865A pdb=" N PHE B 173 " --> pdb=" O GLY B 170 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA B 174 " --> pdb=" O GLY B 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 170 through 174' Processing helix chain 'B' and resid 198 through 209 Processing helix chain 'B' and resid 215 through 244 removed outlier: 3.946A pdb=" N TRP B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) Proline residue: B 241 - end of helix Processing helix chain 'B' and resid 245 through 247 No H-bonds generated for 'chain 'B' and resid 245 through 247' Processing helix chain 'B' and resid 251 through 263 Processing helix chain 'B' and resid 264 through 285 removed outlier: 5.871A pdb=" N SER B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ALA B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 299 removed outlier: 4.377A pdb=" N VAL B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY B 299 " --> pdb=" O VAL B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 341 Processing helix chain 'B' and resid 346 through 361 removed outlier: 3.726A pdb=" N VAL B 353 " --> pdb=" O GLY B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 408 Processing helix chain 'B' and resid 416 through 427 Processing helix chain 'B' and resid 452 through 463 Processing helix chain 'B' and resid 474 through 486 removed outlier: 3.655A pdb=" N ALA B 480 " --> pdb=" O LEU B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 509 removed outlier: 3.779A pdb=" N GLU B 509 " --> pdb=" O GLN B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 529 Processing helix chain 'B' and resid 538 through 543 Processing helix chain 'B' and resid 556 through 582 removed outlier: 3.918A pdb=" N GLU B 560 " --> pdb=" O THR B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 595 Proline residue: B 592 - end of helix Processing helix chain 'B' and resid 599 through 606 removed outlier: 3.805A pdb=" N ASN B 603 " --> pdb=" O PRO B 600 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA B 604 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 631 removed outlier: 4.152A pdb=" N ILE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 638 Processing helix chain 'B' and resid 645 through 680 removed outlier: 4.231A pdb=" N LEU B 659 " --> pdb=" O TRP B 655 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY B 660 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Proline residue: B 665 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 205 Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 45 removed outlier: 4.497A pdb=" N GLY C 51 " --> pdb=" O ILE C 43 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLU C 45 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N VAL C 49 " --> pdb=" O GLU C 45 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 131 through 132 Processing sheet with id=AA5, first strand: chain 'B' and resid 108 through 109 Processing sheet with id=AA6, first strand: chain 'B' and resid 131 through 134 removed outlier: 3.631A pdb=" N LEU B 187 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N VAL B 188 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG B 181 " --> pdb=" O ASP B 154 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 131 through 134 removed outlier: 3.631A pdb=" N LEU B 187 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N VAL B 188 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA B 151 " --> pdb=" O ARG B 167 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG B 167 " --> pdb=" O ALA B 151 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 287 through 288 removed outlier: 7.377A pdb=" N ASP B 550 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ALA B 534 " --> pdb=" O ASP B 550 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 531 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU B 304 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ILE B 470 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N THR B 467 " --> pdb=" O ASP B 489 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N LEU B 491 " --> pdb=" O THR B 467 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N MET B 469 " --> pdb=" O LEU B 491 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 317 through 321 removed outlier: 3.581A pdb=" N SER B 320 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ALA B 444 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL B 439 " --> pdb=" O GLU B 435 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N GLU B 435 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N GLY B 441 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B 433 " --> pdb=" O GLY B 441 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR B 429 " --> pdb=" O LEU B 445 " (cutoff:3.500A) 670 hydrogen bonds defined for protein. 1965 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.07 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 3520 1.34 - 1.49: 2621 1.49 - 1.63: 4969 1.63 - 1.77: 1 1.77 - 1.91: 115 Bond restraints: 11226 Sorted by residual: bond pdb=" OA3 CDL A 609 " pdb=" PA1 CDL A 609 " ideal model delta sigma weight residual 1.529 1.503 0.026 1.00e-02 1.00e+04 6.78e+00 bond pdb=" OB3 CDL A 608 " pdb=" PB2 CDL A 608 " ideal model delta sigma weight residual 1.529 1.503 0.026 1.00e-02 1.00e+04 6.77e+00 bond pdb=" OB3 CDL A 609 " pdb=" PB2 CDL A 609 " ideal model delta sigma weight residual 1.529 1.503 0.026 1.00e-02 1.00e+04 6.51e+00 bond pdb=" OA3 CDL A 608 " pdb=" PA1 CDL A 608 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.38e+00 bond pdb=" C11 CDL A 608 " pdb=" C12 CDL A 608 " ideal model delta sigma weight residual 1.523 1.492 0.031 1.50e-02 4.44e+03 4.29e+00 ... (remaining 11221 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 14799 2.08 - 4.17: 342 4.17 - 6.25: 57 6.25 - 8.33: 30 8.33 - 10.41: 5 Bond angle restraints: 15233 Sorted by residual: angle pdb=" C LEU A 261 " pdb=" N ILE A 262 " pdb=" CA ILE A 262 " ideal model delta sigma weight residual 120.24 122.82 -2.58 6.30e-01 2.52e+00 1.68e+01 angle pdb=" C PRO C 35 " pdb=" N TRP C 36 " pdb=" CA TRP C 36 " ideal model delta sigma weight residual 121.54 128.78 -7.24 1.91e+00 2.74e-01 1.44e+01 angle pdb=" C ASN B 547 " pdb=" N MET B 548 " pdb=" CA MET B 548 " ideal model delta sigma weight residual 121.54 128.77 -7.23 1.91e+00 2.74e-01 1.43e+01 angle pdb=" N VAL B 664 " pdb=" CA VAL B 664 " pdb=" C VAL B 664 " ideal model delta sigma weight residual 108.88 116.65 -7.77 2.16e+00 2.14e-01 1.29e+01 angle pdb=" C ALA B 210 " pdb=" N GLN B 211 " pdb=" CA GLN B 211 " ideal model delta sigma weight residual 122.08 127.11 -5.03 1.47e+00 4.63e-01 1.17e+01 ... (remaining 15228 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 5887 17.41 - 34.82: 617 34.82 - 52.22: 150 52.22 - 69.63: 38 69.63 - 87.04: 11 Dihedral angle restraints: 6703 sinusoidal: 2591 harmonic: 4112 Sorted by residual: dihedral pdb=" CA ALA A 470 " pdb=" C ALA A 470 " pdb=" N PHE A 471 " pdb=" CA PHE A 471 " ideal model delta harmonic sigma weight residual 180.00 156.74 23.26 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA LEU B 183 " pdb=" C LEU B 183 " pdb=" N SER B 184 " pdb=" CA SER B 184 " ideal model delta harmonic sigma weight residual 180.00 -159.15 -20.85 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA PHE C 34 " pdb=" C PHE C 34 " pdb=" N PRO C 35 " pdb=" CA PRO C 35 " ideal model delta harmonic sigma weight residual 180.00 161.09 18.91 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 6700 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1420 0.055 - 0.109: 331 0.109 - 0.164: 55 0.164 - 0.218: 5 0.218 - 0.273: 3 Chirality restraints: 1814 Sorted by residual: chirality pdb=" CB VAL B 664 " pdb=" CA VAL B 664 " pdb=" CG1 VAL B 664 " pdb=" CG2 VAL B 664 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CB VAL B 14 " pdb=" CA VAL B 14 " pdb=" CG1 VAL B 14 " pdb=" CG2 VAL B 14 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA THR A 424 " pdb=" N THR A 424 " pdb=" C THR A 424 " pdb=" CB THR A 424 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1811 not shown) Planarity restraints: 1912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 323 " 0.082 5.00e-02 4.00e+02 1.23e-01 2.42e+01 pdb=" N PRO B 324 " -0.213 5.00e-02 4.00e+02 pdb=" CA PRO B 324 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO B 324 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 429 " -0.037 5.00e-02 4.00e+02 5.60e-02 5.02e+00 pdb=" N PRO B 430 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 430 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 430 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 361 " 0.035 5.00e-02 4.00e+02 5.20e-02 4.33e+00 pdb=" N PRO A 362 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 362 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 362 " 0.029 5.00e-02 4.00e+02 ... (remaining 1909 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.85: 3606 2.85 - 3.42: 12158 3.42 - 3.99: 21567 3.99 - 4.57: 30898 4.57 - 5.14: 44518 Nonbonded interactions: 112747 Sorted by model distance: nonbonded pdb=" OG SER B 615 " pdb=" OD1 ASP B 673 " model vdw 2.272 3.040 nonbonded pdb=" O TYR C 22 " pdb=" OG1 THR C 26 " model vdw 2.283 3.040 nonbonded pdb=" O GLN B 422 " pdb=" OE1 GLN B 426 " model vdw 2.283 3.040 nonbonded pdb=" O SER A 119 " pdb=" OG1 THR A 123 " model vdw 2.284 3.040 nonbonded pdb=" OG SER A 462 " pdb=" O SER A 469 " model vdw 2.315 3.040 ... (remaining 112742 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.920 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 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 0.066 11226 Z= 0.211 Angle : 0.809 10.413 15233 Z= 0.413 Chirality : 0.048 0.273 1814 Planarity : 0.006 0.123 1912 Dihedral : 15.862 87.042 4061 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.20), residues: 1441 helix: -0.14 (0.16), residues: 856 sheet: -0.24 (0.64), residues: 76 loop : -1.13 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 363 TYR 0.035 0.002 TYR A 555 PHE 0.027 0.002 PHE A 260 TRP 0.014 0.001 TRP A 115 HIS 0.003 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.21 (11226) covalent geometry : angle 0.80924 / 0.41 (15233) hydrogen bonds : bond 0.09802 / 5.98 ( 664) hydrogen bonds : angle 5.33758 / 3.80 ( 1965) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 287 MET cc_start: 0.8426 (mtt) cc_final: 0.8179 (mtt) REVERT: A 383 MET cc_start: 0.8289 (tpp) cc_final: 0.7901 (tpt) REVERT: B 469 MET cc_start: 0.7216 (tmm) cc_final: 0.6963 (tmm) REVERT: B 490 PHE cc_start: 0.7425 (p90) cc_final: 0.7138 (p90) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.0949 time to fit residues: 21.7515 Evaluate side-chains 122 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.0970 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.0470 chunk 55 optimal weight: 2.9990 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 80 GLN B 217 ASN B 390 ASN ** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 GLN B 624 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.146310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.119667 restraints weight = 13525.720| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.22 r_work: 0.3221 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11226 Z= 0.105 Angle : 0.501 6.755 15233 Z= 0.255 Chirality : 0.038 0.136 1814 Planarity : 0.004 0.078 1912 Dihedral : 10.303 59.677 1677 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.70 % Allowed : 6.43 % Favored : 92.87 % 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: 0.51 (0.22), residues: 1441 helix: 1.23 (0.17), residues: 852 sheet: -0.54 (0.67), residues: 66 loop : -0.98 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 363 TYR 0.015 0.001 TYR A 381 PHE 0.019 0.001 PHE B 199 TRP 0.008 0.001 TRP B 655 HIS 0.002 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (11226) covalent geometry : angle 0.50132 / 0.26 (15233) hydrogen bonds : bond 0.03457 / 2.20 ( 664) hydrogen bonds : angle 4.29704 / 3.10 ( 1965) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 0.416 Fit side-chains REVERT: A 227 MET cc_start: 0.8328 (mmm) cc_final: 0.7970 (mmm) REVERT: A 383 MET cc_start: 0.8667 (tpp) cc_final: 0.8381 (tpt) REVERT: B 490 PHE cc_start: 0.7767 (p90) cc_final: 0.7472 (p90) outliers start: 8 outliers final: 7 residues processed: 134 average time/residue: 0.0945 time to fit residues: 19.2580 Evaluate side-chains 124 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 122 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 74 optimal weight: 0.4980 chunk 28 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 110 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 96 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS B 217 ASN B 387 ASN B 390 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.142950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.114806 restraints weight = 13696.894| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.28 r_work: 0.3140 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11226 Z= 0.113 Angle : 0.486 6.897 15233 Z= 0.247 Chirality : 0.039 0.144 1814 Planarity : 0.004 0.062 1912 Dihedral : 9.621 59.896 1677 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.23 % Allowed : 8.54 % Favored : 90.23 % 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: 0.95 (0.22), residues: 1441 helix: 1.62 (0.18), residues: 854 sheet: -0.46 (0.63), residues: 73 loop : -0.87 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 363 TYR 0.018 0.001 TYR A 381 PHE 0.009 0.001 PHE A 527 TRP 0.008 0.001 TRP B 71 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (11226) covalent geometry : angle 0.48577 / 0.25 (15233) hydrogen bonds : bond 0.03401 / 2.16 ( 664) hydrogen bonds : angle 4.16022 / 3.02 ( 1965) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.415 Fit side-chains REVERT: A 71 MET cc_start: 0.8418 (mmp) cc_final: 0.8198 (mmt) REVERT: A 227 MET cc_start: 0.8442 (mmm) cc_final: 0.8106 (mmm) REVERT: A 383 MET cc_start: 0.8683 (tpp) cc_final: 0.8401 (tpt) REVERT: A 439 ASP cc_start: 0.8649 (OUTLIER) cc_final: 0.8304 (t0) REVERT: A 445 MET cc_start: 0.7118 (mmm) cc_final: 0.6909 (mmm) REVERT: C 1 MET cc_start: 0.4149 (mmt) cc_final: 0.3932 (mmm) REVERT: C 32 TRP cc_start: 0.8293 (t60) cc_final: 0.8092 (t60) REVERT: C 128 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9128 (mp) REVERT: B 490 PHE cc_start: 0.7820 (p90) cc_final: 0.7538 (p90) outliers start: 14 outliers final: 10 residues processed: 132 average time/residue: 0.1041 time to fit residues: 20.3292 Evaluate side-chains 127 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 141 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 136 optimal weight: 0.1980 chunk 32 optimal weight: 0.0870 chunk 50 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 99 optimal weight: 0.8980 chunk 124 optimal weight: 0.4980 chunk 85 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS B 217 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.144757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.117210 restraints weight = 13614.647| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.14 r_work: 0.3139 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11226 Z= 0.097 Angle : 0.469 6.861 15233 Z= 0.238 Chirality : 0.038 0.138 1814 Planarity : 0.003 0.053 1912 Dihedral : 9.175 59.426 1677 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.23 % Allowed : 10.12 % Favored : 88.64 % 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: 1.20 (0.22), residues: 1441 helix: 1.86 (0.18), residues: 856 sheet: -0.44 (0.63), residues: 73 loop : -0.84 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 363 TYR 0.016 0.001 TYR A 381 PHE 0.008 0.001 PHE A 527 TRP 0.008 0.001 TRP B 71 HIS 0.002 0.000 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (11226) covalent geometry : angle 0.46890 / 0.24 (15233) hydrogen bonds : bond 0.03234 / 2.06 ( 664) hydrogen bonds : angle 4.05894 / 2.95 ( 1965) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.413 Fit side-chains REVERT: A 227 MET cc_start: 0.8349 (mmm) cc_final: 0.8011 (mmm) REVERT: A 383 MET cc_start: 0.8671 (tpp) cc_final: 0.8358 (tpt) REVERT: A 439 ASP cc_start: 0.8609 (OUTLIER) cc_final: 0.8247 (t0) REVERT: C 1 MET cc_start: 0.4205 (mmt) cc_final: 0.3982 (mmm) REVERT: C 32 TRP cc_start: 0.8260 (t60) cc_final: 0.8023 (t60) REVERT: B 490 PHE cc_start: 0.7733 (p90) cc_final: 0.7517 (p90) outliers start: 14 outliers final: 11 residues processed: 136 average time/residue: 0.0932 time to fit residues: 19.2458 Evaluate side-chains 134 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 85 optimal weight: 4.9990 chunk 30 optimal weight: 0.3980 chunk 41 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.143274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.116506 restraints weight = 13571.436| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.22 r_work: 0.3100 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11226 Z= 0.105 Angle : 0.475 6.838 15233 Z= 0.239 Chirality : 0.038 0.136 1814 Planarity : 0.003 0.049 1912 Dihedral : 8.743 59.922 1677 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.41 % Allowed : 11.62 % Favored : 86.97 % 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: 1.25 (0.22), residues: 1441 helix: 1.89 (0.18), residues: 863 sheet: -0.35 (0.64), residues: 73 loop : -0.86 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 50 TYR 0.016 0.001 TYR A 381 PHE 0.009 0.001 PHE A 527 TRP 0.008 0.001 TRP B 71 HIS 0.002 0.000 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 (11226) covalent geometry : angle 0.47472 / 0.24 (15233) hydrogen bonds : bond 0.03219 / 2.06 ( 664) hydrogen bonds : angle 4.02394 / 2.93 ( 1965) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.458 Fit side-chains REVERT: A 227 MET cc_start: 0.8416 (mmm) cc_final: 0.8107 (mmm) REVERT: A 383 MET cc_start: 0.8687 (tpp) cc_final: 0.8380 (tpt) REVERT: A 439 ASP cc_start: 0.8577 (OUTLIER) cc_final: 0.8228 (t0) REVERT: C 1 MET cc_start: 0.4167 (mmt) cc_final: 0.3944 (mmm) REVERT: C 32 TRP cc_start: 0.8325 (t60) cc_final: 0.8088 (t60) REVERT: B 490 PHE cc_start: 0.7767 (p90) cc_final: 0.7544 (p90) outliers start: 16 outliers final: 11 residues processed: 133 average time/residue: 0.1040 time to fit residues: 20.5332 Evaluate side-chains 132 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain C residue 157 GLN Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 48 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 125 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS B 624 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.142314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.116401 restraints weight = 13638.272| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.25 r_work: 0.3098 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11226 Z= 0.114 Angle : 0.480 6.800 15233 Z= 0.242 Chirality : 0.039 0.188 1814 Planarity : 0.003 0.047 1912 Dihedral : 8.369 58.047 1677 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.94 % Allowed : 11.62 % Favored : 86.44 % 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: 1.26 (0.22), residues: 1441 helix: 1.91 (0.18), residues: 865 sheet: -0.36 (0.64), residues: 73 loop : -0.90 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 50 TYR 0.016 0.001 TYR A 381 PHE 0.009 0.001 PHE A 527 TRP 0.008 0.001 TRP B 71 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (11226) covalent geometry : angle 0.48046 / 0.24 (15233) hydrogen bonds : bond 0.03282 / 2.10 ( 664) hydrogen bonds : angle 4.02718 / 2.94 ( 1965) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.414 Fit side-chains REVERT: A 227 MET cc_start: 0.8507 (mmm) cc_final: 0.8213 (mmm) REVERT: A 383 MET cc_start: 0.8768 (tpp) cc_final: 0.8457 (tpt) REVERT: A 439 ASP cc_start: 0.8611 (OUTLIER) cc_final: 0.8277 (t0) REVERT: A 445 MET cc_start: 0.7593 (mmm) cc_final: 0.7002 (mmm) REVERT: C 32 TRP cc_start: 0.8372 (t60) cc_final: 0.8142 (t60) outliers start: 22 outliers final: 15 residues processed: 135 average time/residue: 0.1004 time to fit residues: 20.1473 Evaluate side-chains 134 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 134 optimal weight: 0.5980 chunk 60 optimal weight: 0.0670 chunk 119 optimal weight: 10.0000 chunk 139 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 chunk 112 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 34 optimal weight: 0.0570 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS B 390 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.143300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.114605 restraints weight = 13519.480| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.22 r_work: 0.3069 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11226 Z= 0.097 Angle : 0.468 6.800 15233 Z= 0.236 Chirality : 0.038 0.133 1814 Planarity : 0.003 0.046 1912 Dihedral : 8.059 57.520 1677 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.67 % Allowed : 12.24 % Favored : 86.09 % 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: 1.42 (0.22), residues: 1441 helix: 2.03 (0.18), residues: 866 sheet: -0.33 (0.64), residues: 73 loop : -0.80 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 44 TYR 0.015 0.001 TYR A 381 PHE 0.008 0.001 PHE A 527 TRP 0.008 0.001 TRP B 71 HIS 0.003 0.000 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (11226) covalent geometry : angle 0.46759 / 0.24 (15233) hydrogen bonds : bond 0.03135 / 2.00 ( 664) hydrogen bonds : angle 3.96775 / 2.89 ( 1965) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.422 Fit side-chains REVERT: A 227 MET cc_start: 0.8394 (mmm) cc_final: 0.8072 (mmm) REVERT: A 383 MET cc_start: 0.8657 (tpp) cc_final: 0.8388 (tpt) REVERT: A 439 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.8211 (t0) REVERT: C 32 TRP cc_start: 0.8377 (t60) cc_final: 0.8116 (t60) REVERT: B 403 ARG cc_start: 0.6714 (tpp80) cc_final: 0.6397 (ttp-170) outliers start: 19 outliers final: 14 residues processed: 132 average time/residue: 0.0994 time to fit residues: 19.6283 Evaluate side-chains 134 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 157 GLN Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 77 optimal weight: 0.4980 chunk 136 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 ASN C 66 HIS B 390 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.134281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.104973 restraints weight = 13782.802| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.20 r_work: 0.2949 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 11226 Z= 0.221 Angle : 0.575 7.019 15233 Z= 0.292 Chirality : 0.042 0.141 1814 Planarity : 0.004 0.060 1912 Dihedral : 8.548 59.947 1677 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.67 % Allowed : 12.24 % Favored : 86.09 % 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: 0.91 (0.22), residues: 1441 helix: 1.56 (0.17), residues: 862 sheet: -0.06 (0.61), residues: 76 loop : -0.97 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 44 TYR 0.027 0.002 TYR A 381 PHE 0.013 0.002 PHE A 270 TRP 0.009 0.001 TRP B 71 HIS 0.006 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.22 (11226) covalent geometry : angle 0.57458 / 0.29 (15233) hydrogen bonds : bond 0.04077 / 2.60 ( 664) hydrogen bonds : angle 4.36086 / 3.18 ( 1965) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.466 Fit side-chains REVERT: A 227 MET cc_start: 0.8684 (mmm) cc_final: 0.8358 (mmm) REVERT: A 287 MET cc_start: 0.8949 (mtt) cc_final: 0.8724 (mtt) REVERT: A 383 MET cc_start: 0.8686 (tpp) cc_final: 0.8442 (tpt) REVERT: A 439 ASP cc_start: 0.8526 (OUTLIER) cc_final: 0.8241 (t0) REVERT: C 1 MET cc_start: 0.4164 (mmt) cc_final: 0.3918 (mmm) REVERT: C 32 TRP cc_start: 0.8477 (t60) cc_final: 0.8240 (t60) REVERT: B 213 ARG cc_start: 0.6901 (tpm170) cc_final: 0.6455 (tpp-160) REVERT: B 360 PHE cc_start: 0.5731 (t80) cc_final: 0.5474 (t80) outliers start: 19 outliers final: 14 residues processed: 131 average time/residue: 0.0986 time to fit residues: 19.3862 Evaluate side-chains 130 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 157 GLN Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 86 optimal weight: 9.9990 chunk 4 optimal weight: 2.9990 chunk 76 optimal weight: 0.0770 chunk 56 optimal weight: 0.6980 chunk 93 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 140 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 120 optimal weight: 0.6980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN B 624 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.137353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.108696 restraints weight = 13712.150| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.24 r_work: 0.3019 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11226 Z= 0.106 Angle : 0.491 6.906 15233 Z= 0.249 Chirality : 0.039 0.140 1814 Planarity : 0.003 0.044 1912 Dihedral : 7.992 59.596 1677 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.41 % Allowed : 12.76 % Favored : 85.83 % 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: 1.25 (0.22), residues: 1441 helix: 1.85 (0.18), residues: 868 sheet: -0.60 (0.63), residues: 75 loop : -0.76 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 44 TYR 0.018 0.001 TYR A 381 PHE 0.010 0.001 PHE A 260 TRP 0.009 0.001 TRP A 115 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (11226) covalent geometry : angle 0.49063 / 0.25 (15233) hydrogen bonds : bond 0.03341 / 2.13 ( 664) hydrogen bonds : angle 4.12464 / 3.01 ( 1965) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.415 Fit side-chains REVERT: A 227 MET cc_start: 0.8492 (mmm) cc_final: 0.8153 (mmm) REVERT: A 287 MET cc_start: 0.8791 (mtt) cc_final: 0.8555 (mtt) REVERT: A 383 MET cc_start: 0.8641 (tpp) cc_final: 0.8338 (tpt) REVERT: A 439 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.8236 (t0) REVERT: C 32 TRP cc_start: 0.8471 (t60) cc_final: 0.8230 (t60) REVERT: B 213 ARG cc_start: 0.6697 (tpm170) cc_final: 0.6286 (tpp-160) REVERT: B 360 PHE cc_start: 0.5879 (t80) cc_final: 0.5634 (t80) REVERT: B 403 ARG cc_start: 0.6823 (tpp80) cc_final: 0.6336 (ttp-170) outliers start: 16 outliers final: 14 residues processed: 130 average time/residue: 0.0950 time to fit residues: 18.4162 Evaluate side-chains 129 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 157 GLN Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS B 653 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.139039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.110792 restraints weight = 13760.154| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.18 r_work: 0.3018 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11226 Z= 0.121 Angle : 0.497 6.921 15233 Z= 0.251 Chirality : 0.039 0.133 1814 Planarity : 0.003 0.044 1912 Dihedral : 7.841 59.770 1677 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.58 % Allowed : 12.41 % Favored : 86.00 % 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: 1.28 (0.22), residues: 1441 helix: 1.90 (0.18), residues: 862 sheet: -0.34 (0.66), residues: 73 loop : -0.81 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 44 TYR 0.018 0.001 TYR A 381 PHE 0.009 0.001 PHE A 527 TRP 0.010 0.001 TRP A 115 HIS 0.005 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (11226) covalent geometry : angle 0.49669 / 0.25 (15233) hydrogen bonds : bond 0.03378 / 2.16 ( 664) hydrogen bonds : angle 4.12512 / 3.01 ( 1965) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.411 Fit side-chains REVERT: A 227 MET cc_start: 0.8546 (mmm) cc_final: 0.8232 (mmm) REVERT: A 287 MET cc_start: 0.8851 (mtt) cc_final: 0.8612 (mtt) REVERT: A 383 MET cc_start: 0.8676 (tpp) cc_final: 0.8385 (tpt) REVERT: A 439 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.8237 (t0) REVERT: C 32 TRP cc_start: 0.8459 (t60) cc_final: 0.8224 (t60) REVERT: B 213 ARG cc_start: 0.6781 (tpm170) cc_final: 0.6414 (tpp-160) REVERT: B 360 PHE cc_start: 0.5893 (t80) cc_final: 0.5648 (t80) REVERT: B 392 MET cc_start: 0.6357 (tpt) cc_final: 0.5971 (tpt) REVERT: B 403 ARG cc_start: 0.6886 (tpp80) cc_final: 0.6377 (ttp-170) outliers start: 18 outliers final: 14 residues processed: 129 average time/residue: 0.0882 time to fit residues: 17.0505 Evaluate side-chains 130 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 157 GLN Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 15 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 99 optimal weight: 0.2980 chunk 86 optimal weight: 8.9990 chunk 12 optimal weight: 0.6980 chunk 92 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS B 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.139334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.110840 restraints weight = 13774.756| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.23 r_work: 0.3038 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11226 Z= 0.107 Angle : 0.484 6.889 15233 Z= 0.244 Chirality : 0.038 0.133 1814 Planarity : 0.003 0.044 1912 Dihedral : 7.491 58.707 1677 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.50 % Allowed : 12.50 % Favored : 86.00 % 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: 1.41 (0.23), residues: 1441 helix: 2.00 (0.18), residues: 863 sheet: -0.45 (0.64), residues: 75 loop : -0.72 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 44 TYR 0.017 0.001 TYR A 381 PHE 0.009 0.001 PHE A 527 TRP 0.009 0.001 TRP A 115 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (11226) covalent geometry : angle 0.48365 / 0.24 (15233) hydrogen bonds : bond 0.03222 / 2.06 ( 664) hydrogen bonds : angle 4.05757 / 2.97 ( 1965) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2625.09 seconds wall clock time: 45 minutes 54.56 seconds (2754.56 seconds total)