Starting phenix.real_space_refine on Wed Mar 4 09:08:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zrd_14911/03_2026/7zrd_14911.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zrd_14911/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7zrd_14911/03_2026/7zrd_14911.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zrd_14911/03_2026/7zrd_14911.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zrd_14911/03_2026/7zrd_14911.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zrd_14911/03_2026/7zrd_14911.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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-5986/lib/python3.9/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: 2.38, per 1000 atoms: 0.22 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: 1.05 Conformation dependent library (CDL) restraints added in 625.5 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: 0.38 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: 1.81 Time building geometry restraints manager: 1.43 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: 5893 17.41 - 34.82: 631 34.82 - 52.22: 166 52.22 - 69.63: 41 69.63 - 87.04: 12 Dihedral angle restraints: 6743 sinusoidal: 2631 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 6740 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.960 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 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 : 16.186 87.042 4101 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 covalent geometry : bond 0.00433 (11226) covalent geometry : angle 0.80924 (15233) hydrogen bonds : bond 0.09802 ( 664) hydrogen bonds : angle 5.33758 ( 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 : 0.407 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: 0.0998 time to fit residues: 22.5110 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 : 0.331 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3652 r_free = 0.3652 target = 0.146285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.119477 restraints weight = 13528.428| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.21 r_work: 0.3151 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.0883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11226 Z= 0.106 Angle : 0.505 6.736 15233 Z= 0.256 Chirality : 0.038 0.138 1814 Planarity : 0.004 0.079 1912 Dihedral : 11.191 62.013 1717 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.04 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: 0.50 (0.22), residues: 1441 helix: 1.21 (0.17), residues: 852 sheet: -0.53 (0.67), residues: 66 loop : -0.98 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 572 TYR 0.015 0.001 TYR A 381 PHE 0.018 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 covalent geometry : bond 0.00227 (11226) covalent geometry : angle 0.50452 (15233) hydrogen bonds : bond 0.03507 ( 664) hydrogen bonds : angle 4.31119 ( 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 : 0.475 Fit side-chains REVERT: A 227 MET cc_start: 0.8345 (mmm) cc_final: 0.8030 (mmm) REVERT: A 383 MET cc_start: 0.8648 (tpp) cc_final: 0.8385 (tpt) REVERT: B 490 PHE cc_start: 0.7796 (p90) cc_final: 0.7472 (p90) outliers start: 8 outliers final: 7 residues processed: 134 average time/residue: 0.0976 time to fit residues: 19.7692 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 : 0.421 ------------------------------------------------------------------------------- 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: 4.9990 chunk 6 optimal weight: 3.9990 chunk 62 optimal weight: 0.1980 chunk 18 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 96 optimal weight: 9.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3595 r_free = 0.3595 target = 0.141439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.114305 restraints weight = 13660.234| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.16 r_work: 0.3118 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11226 Z= 0.140 Angle : 0.509 6.934 15233 Z= 0.259 Chirality : 0.039 0.148 1814 Planarity : 0.004 0.063 1912 Dihedral : 10.453 63.615 1717 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.23 % Allowed : 8.63 % Favored : 90.14 % 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: 0.86 (0.22), residues: 1441 helix: 1.54 (0.18), residues: 853 sheet: -0.51 (0.63), residues: 73 loop : -0.89 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 572 TYR 0.020 0.001 TYR A 381 PHE 0.010 0.001 PHE A 527 TRP 0.009 0.001 TRP B 71 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00328 (11226) covalent geometry : angle 0.50948 (15233) hydrogen bonds : bond 0.03628 ( 664) hydrogen bonds : angle 4.24561 ( 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 139 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.466 Fit side-chains REVERT: A 71 MET cc_start: 0.8385 (mmp) cc_final: 0.8159 (mmt) REVERT: A 227 MET cc_start: 0.8479 (mmm) cc_final: 0.8131 (mmm) REVERT: A 287 MET cc_start: 0.8840 (mtt) cc_final: 0.8608 (mtt) REVERT: A 383 MET cc_start: 0.8720 (tpp) cc_final: 0.8383 (tpt) REVERT: A 439 ASP cc_start: 0.8629 (OUTLIER) cc_final: 0.8284 (t0) REVERT: B 490 PHE cc_start: 0.7760 (p90) cc_final: 0.7529 (p90) outliers start: 14 outliers final: 11 residues processed: 134 average time/residue: 0.1025 time to fit residues: 20.4922 Evaluate side-chains 129 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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: 0.8980 chunk 55 optimal weight: 0.6980 chunk 136 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 90 optimal weight: 0.0030 chunk 116 optimal weight: 10.0000 chunk 99 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 69 optimal weight: 0.0570 overall best weight: 0.4908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3615 r_free = 0.3615 target = 0.143083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.115409 restraints weight = 13651.866| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.23 r_work: 0.3098 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11226 Z= 0.099 Angle : 0.474 6.867 15233 Z= 0.241 Chirality : 0.038 0.138 1814 Planarity : 0.003 0.055 1912 Dihedral : 10.059 60.177 1717 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.23 % Allowed : 10.48 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.22), residues: 1441 helix: 1.83 (0.18), residues: 855 sheet: -0.45 (0.63), residues: 73 loop : -0.82 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 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 0.002 0.000 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00216 (11226) covalent geometry : angle 0.47435 (15233) hydrogen bonds : bond 0.03279 ( 664) hydrogen bonds : angle 4.08961 ( 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 140 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.355 Fit side-chains REVERT: A 227 MET cc_start: 0.8400 (mmm) cc_final: 0.8058 (mmm) REVERT: A 383 MET cc_start: 0.8628 (tpp) cc_final: 0.8338 (tpt) REVERT: A 439 ASP cc_start: 0.8621 (OUTLIER) cc_final: 0.8256 (t0) REVERT: C 1 MET cc_start: 0.4227 (mmt) cc_final: 0.4009 (mmm) REVERT: B 490 PHE cc_start: 0.7762 (p90) cc_final: 0.7515 (p90) outliers start: 14 outliers final: 9 residues processed: 135 average time/residue: 0.0887 time to fit residues: 18.2773 Evaluate side-chains 130 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 0.264 ------------------------------------------------------------------------------- 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 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: 8.9990 chunk 30 optimal weight: 0.2980 chunk 41 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 123 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3606 r_free = 0.3606 target = 0.142229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.115057 restraints weight = 13538.462| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.11 r_work: 0.3137 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1482 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= 0.111 Angle : 0.480 6.844 15233 Z= 0.243 Chirality : 0.039 0.140 1814 Planarity : 0.003 0.050 1912 Dihedral : 9.724 59.529 1717 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.67 % Allowed : 11.53 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.22), residues: 1441 helix: 1.87 (0.18), residues: 861 sheet: -0.38 (0.63), residues: 73 loop : -0.82 (0.27), residues: 507 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 0.008 0.001 TRP B 71 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00254 (11226) covalent geometry : angle 0.48029 (15233) hydrogen bonds : bond 0.03304 ( 664) hydrogen bonds : angle 4.06090 ( 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 145 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.299 Fit side-chains REVERT: A 227 MET cc_start: 0.8431 (mmm) cc_final: 0.8101 (mmm) REVERT: A 287 MET cc_start: 0.8840 (mtt) cc_final: 0.8596 (mtt) REVERT: A 383 MET cc_start: 0.8710 (tpp) cc_final: 0.8375 (tpt) REVERT: A 439 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8201 (t0) REVERT: C 1 MET cc_start: 0.4431 (mmt) cc_final: 0.4200 (mmm) outliers start: 19 outliers final: 16 residues processed: 136 average time/residue: 0.0939 time to fit residues: 18.9042 Evaluate side-chains 138 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 48 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3527 r_free = 0.3527 target = 0.135708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.107097 restraints weight = 13820.665| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.24 r_work: 0.2976 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11226 Z= 0.180 Angle : 0.546 6.963 15233 Z= 0.278 Chirality : 0.041 0.138 1814 Planarity : 0.004 0.049 1912 Dihedral : 9.902 59.382 1717 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.76 % Allowed : 12.06 % Favored : 86.18 % 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: 1.58 (0.18), residues: 868 sheet: -0.02 (0.61), residues: 76 loop : -1.05 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 44 TYR 0.021 0.002 TYR A 381 PHE 0.011 0.001 PHE A 270 TRP 0.010 0.001 TRP A 115 HIS 0.006 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00432 (11226) covalent geometry : angle 0.54635 (15233) hydrogen bonds : bond 0.03860 ( 664) hydrogen bonds : angle 4.30151 ( 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 135 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.417 Fit side-chains REVERT: A 227 MET cc_start: 0.8662 (mmm) cc_final: 0.8348 (mmm) REVERT: A 287 MET cc_start: 0.8898 (mtt) cc_final: 0.8666 (mtt) REVERT: A 383 MET cc_start: 0.8695 (tpp) cc_final: 0.8413 (tpt) REVERT: A 439 ASP cc_start: 0.8572 (OUTLIER) cc_final: 0.8280 (t0) REVERT: B 213 ARG cc_start: 0.6824 (tpm170) cc_final: 0.6380 (tpp-160) REVERT: B 360 PHE cc_start: 0.5924 (t80) cc_final: 0.5640 (t80) REVERT: B 403 ARG cc_start: 0.6809 (tpp80) cc_final: 0.6461 (ttp-170) REVERT: B 490 PHE cc_start: 0.7807 (OUTLIER) cc_final: 0.7467 (p90) outliers start: 20 outliers final: 13 residues processed: 127 average time/residue: 0.0918 time to fit residues: 17.3754 Evaluate side-chains 128 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 MET 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 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 471 THR Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 548 MET 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: 3.9990 chunk 60 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 139 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.134249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.105286 restraints weight = 13762.700| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.28 r_work: 0.2949 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 11226 Z= 0.208 Angle : 0.565 7.046 15233 Z= 0.287 Chirality : 0.042 0.142 1814 Planarity : 0.004 0.057 1912 Dihedral : 10.107 59.628 1717 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.29 % Allowed : 11.88 % 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: 0.70 (0.22), residues: 1441 helix: 1.43 (0.17), residues: 866 sheet: -0.20 (0.60), residues: 76 loop : -1.13 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 281 TYR 0.022 0.002 TYR A 381 PHE 0.013 0.002 PHE A 109 TRP 0.009 0.001 TRP B 71 HIS 0.005 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00505 (11226) covalent geometry : angle 0.56499 (15233) hydrogen bonds : bond 0.04061 ( 664) hydrogen bonds : angle 4.42476 ( 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 140 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.400 Fit side-chains REVERT: A 227 MET cc_start: 0.8709 (mmm) cc_final: 0.8337 (mmm) REVERT: A 287 MET cc_start: 0.8997 (mtt) cc_final: 0.8788 (mtt) REVERT: A 383 MET cc_start: 0.8684 (tpp) cc_final: 0.8382 (tpt) REVERT: A 439 ASP cc_start: 0.8528 (OUTLIER) cc_final: 0.8259 (t0) REVERT: B 213 ARG cc_start: 0.6911 (tpm170) cc_final: 0.6520 (tpp-160) REVERT: B 360 PHE cc_start: 0.5795 (t80) cc_final: 0.5573 (t80) REVERT: B 490 PHE cc_start: 0.7849 (OUTLIER) cc_final: 0.7537 (p90) outliers start: 26 outliers final: 17 residues processed: 131 average time/residue: 0.1032 time to fit residues: 20.1324 Evaluate side-chains 130 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 366 MET 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 490 PHE 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: 0.0040 chunk 136 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 70 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 ASN B 653 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.137202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.108711 restraints weight = 13658.653| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.25 r_work: 0.2986 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2044 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= 0.122 Angle : 0.500 6.897 15233 Z= 0.255 Chirality : 0.039 0.135 1814 Planarity : 0.003 0.045 1912 Dihedral : 9.645 59.412 1717 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.94 % Allowed : 12.32 % Favored : 85.74 % 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: 1.07 (0.22), residues: 1441 helix: 1.71 (0.18), residues: 864 sheet: -0.15 (0.61), residues: 76 loop : -0.92 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 44 TYR 0.018 0.001 TYR A 381 PHE 0.010 0.001 PHE A 109 TRP 0.009 0.001 TRP B 71 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00284 (11226) covalent geometry : angle 0.50046 (15233) hydrogen bonds : bond 0.03502 ( 664) hydrogen bonds : angle 4.23992 ( 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 135 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.404 Fit side-chains REVERT: A 227 MET cc_start: 0.8591 (mmm) cc_final: 0.8238 (mmm) REVERT: A 287 MET cc_start: 0.8878 (mtt) cc_final: 0.8641 (mtt) REVERT: A 383 MET cc_start: 0.8656 (tpp) cc_final: 0.8351 (tpt) REVERT: A 439 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.8213 (t0) REVERT: B 213 ARG cc_start: 0.6898 (tpm170) cc_final: 0.6459 (tpp-160) REVERT: B 360 PHE cc_start: 0.5837 (t80) cc_final: 0.5621 (t80) REVERT: B 403 ARG cc_start: 0.6867 (tpp80) cc_final: 0.6524 (tpp-160) outliers start: 22 outliers final: 16 residues processed: 128 average time/residue: 0.0997 time to fit residues: 19.2920 Evaluate side-chains 128 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 C residue 157 GLN Chi-restraints excluded: chain B residue 18 LEU 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 615 SER 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: 6.9990 chunk 4 optimal weight: 3.9990 chunk 76 optimal weight: 0.0370 chunk 56 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 71 optimal weight: 0.7980 chunk 140 optimal weight: 4.9990 chunk 47 optimal weight: 0.4980 chunk 88 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 overall best weight: 0.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.138793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.113624 restraints weight = 13562.900| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.17 r_work: 0.3041 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11226 Z= 0.119 Angle : 0.496 6.871 15233 Z= 0.252 Chirality : 0.039 0.134 1814 Planarity : 0.003 0.044 1912 Dihedral : 9.342 58.981 1717 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.76 % Allowed : 12.50 % Favored : 85.74 % 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: 1.12 (0.22), residues: 1441 helix: 1.72 (0.18), residues: 870 sheet: -0.19 (0.62), residues: 80 loop : -0.87 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 44 TYR 0.017 0.001 TYR A 381 PHE 0.009 0.001 PHE A 109 TRP 0.010 0.001 TRP B 71 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00278 (11226) covalent geometry : angle 0.49617 (15233) hydrogen bonds : bond 0.03444 ( 664) hydrogen bonds : angle 4.19650 ( 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 133 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.402 Fit side-chains REVERT: A 227 MET cc_start: 0.8583 (mmm) cc_final: 0.8257 (mmm) REVERT: A 287 MET cc_start: 0.8965 (mtt) cc_final: 0.8734 (mtt) REVERT: A 383 MET cc_start: 0.8739 (tpp) cc_final: 0.8404 (tpt) REVERT: A 439 ASP cc_start: 0.8534 (OUTLIER) cc_final: 0.8253 (t0) REVERT: B 213 ARG cc_start: 0.6895 (tpm170) cc_final: 0.6689 (mmp80) outliers start: 20 outliers final: 19 residues processed: 127 average time/residue: 0.1011 time to fit residues: 19.1756 Evaluate side-chains 132 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 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 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 615 SER 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: 0.8980 chunk 42 optimal weight: 0.7980 chunk 69 optimal weight: 0.3980 chunk 19 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3573 r_free = 0.3573 target = 0.139591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.111356 restraints weight = 13716.149| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.27 r_work: 0.3002 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11226 Z= 0.111 Angle : 0.494 6.867 15233 Z= 0.251 Chirality : 0.039 0.146 1814 Planarity : 0.003 0.044 1912 Dihedral : 9.216 59.169 1717 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.94 % Allowed : 12.15 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.22), residues: 1441 helix: 1.74 (0.18), residues: 875 sheet: -0.20 (0.62), residues: 80 loop : -0.81 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 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 B 71 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00257 (11226) covalent geometry : angle 0.49400 (15233) hydrogen bonds : bond 0.03373 ( 664) hydrogen bonds : angle 4.17418 ( 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 137 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.444 Fit side-chains REVERT: A 227 MET cc_start: 0.8535 (mmm) cc_final: 0.8186 (mmm) REVERT: A 287 MET cc_start: 0.8823 (mtt) cc_final: 0.8574 (mtt) REVERT: A 383 MET cc_start: 0.8657 (tpp) cc_final: 0.8356 (tpt) REVERT: A 439 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8219 (t0) REVERT: B 213 ARG cc_start: 0.6863 (tpm170) cc_final: 0.6561 (mmp80) REVERT: B 403 ARG cc_start: 0.6807 (tpp80) cc_final: 0.6309 (ttp-170) outliers start: 22 outliers final: 19 residues processed: 130 average time/residue: 0.0997 time to fit residues: 19.3015 Evaluate side-chains 134 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 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 469 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 15 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 68 optimal weight: 0.3980 chunk 99 optimal weight: 0.7980 chunk 86 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 77 optimal weight: 0.3980 chunk 8 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 80 GLN B 93 GLN B 361 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.140580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.114736 restraints weight = 13643.510| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.22 r_work: 0.3034 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2066 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= 0.108 Angle : 0.497 8.114 15233 Z= 0.251 Chirality : 0.039 0.142 1814 Planarity : 0.003 0.044 1912 Dihedral : 9.044 59.979 1717 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.85 % Allowed : 12.76 % Favored : 85.39 % 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: 1.29 (0.23), residues: 1441 helix: 1.82 (0.18), residues: 877 sheet: -0.12 (0.62), residues: 80 loop : -0.74 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 44 TYR 0.016 0.001 TYR A 381 PHE 0.008 0.001 PHE A 527 TRP 0.009 0.001 TRP B 71 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00245 (11226) covalent geometry : angle 0.49676 (15233) hydrogen bonds : bond 0.03282 ( 664) hydrogen bonds : angle 4.15310 ( 1965) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2663.52 seconds wall clock time: 46 minutes 25.05 seconds (2785.05 seconds total)