Starting phenix.real_space_refine on Wed Jul 30 13:31:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zrd_14911/07_2025/7zrd_14911.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zrd_14911/07_2025/7zrd_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_2025/7zrd_14911.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zrd_14911/07_2025/7zrd_14911.map" model { file = "/net/cci-nas-00/data/ceres_data/7zrd_14911/07_2025/7zrd_14911.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zrd_14911/07_2025/7zrd_14911.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.21, per 1000 atoms: 0.65 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: 2.63 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.34 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: 3.67 Time building geometry restraints manager: 3.12 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 28.790 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.660 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.014 0.001 TRP A 115 HIS 0.003 0.001 HIS A 242 PHE 0.027 0.002 PHE A 260 TYR 0.035 0.002 TYR A 555 ARG 0.015 0.000 ARG B 363 Details of bonding type rmsd hydrogen bonds : bond 0.09802 ( 664) hydrogen bonds : angle 5.33758 ( 1965) covalent geometry : bond 0.00433 (11226) covalent geometry : angle 0.80924 (15233) *********************** 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 : 1.261 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: 0.2145 time to fit residues: 48.2325 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 : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 0.7980 chunk 108 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 37 optimal weight: 0.0370 chunk 73 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 112 optimal weight: 8.9990 chunk 43 optimal weight: 0.0970 chunk 68 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- 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 = 0.3657 r_free = 0.3657 target = 0.146727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.119792 restraints weight = 13397.980| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.24 r_work: 0.3141 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 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 0.034 11226 Z= 0.102 Angle : 0.502 6.742 15233 Z= 0.255 Chirality : 0.038 0.134 1814 Planarity : 0.004 0.078 1912 Dihedral : 11.202 61.828 1717 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.95 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.22), residues: 1441 helix: 1.24 (0.17), residues: 852 sheet: -0.52 (0.67), residues: 66 loop : -0.99 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 655 HIS 0.002 0.001 HIS A 451 PHE 0.018 0.001 PHE B 199 TYR 0.015 0.001 TYR A 381 ARG 0.005 0.000 ARG B 363 Details of bonding type rmsd hydrogen bonds : bond 0.03453 ( 664) hydrogen bonds : angle 4.29502 ( 1965) covalent geometry : bond 0.00223 (11226) covalent geometry : angle 0.50153 (15233) *********************** 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 139 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 1.004 Fit side-chains REVERT: A 227 MET cc_start: 0.8328 (mmm) cc_final: 0.7992 (mmm) REVERT: A 383 MET cc_start: 0.8633 (tpp) cc_final: 0.8375 (tpt) REVERT: B 490 PHE cc_start: 0.7833 (p90) cc_final: 0.7486 (p90) outliers start: 8 outliers final: 7 residues processed: 136 average time/residue: 0.2645 time to fit residues: 53.0663 Evaluate side-chains 125 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 118 time to evaluate : 1.132 ------------------------------------------------------------------------------- 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 77 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 116 optimal weight: 0.2980 chunk 63 optimal weight: 6.9990 chunk 83 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 89 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3639 r_free = 0.3639 target = 0.145137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.117249 restraints weight = 13633.302| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.20 r_work: 0.3170 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1118 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= 0.106 Angle : 0.481 6.850 15233 Z= 0.244 Chirality : 0.038 0.143 1814 Planarity : 0.004 0.062 1912 Dihedral : 10.417 62.763 1717 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.14 % Allowed : 8.45 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.22), residues: 1441 helix: 1.66 (0.18), residues: 854 sheet: -0.44 (0.63), residues: 73 loop : -0.89 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 71 HIS 0.003 0.001 HIS A 451 PHE 0.009 0.001 PHE A 527 TYR 0.018 0.001 TYR A 381 ARG 0.003 0.000 ARG B 363 Details of bonding type rmsd hydrogen bonds : bond 0.03347 ( 664) hydrogen bonds : angle 4.14017 ( 1965) covalent geometry : bond 0.00234 (11226) covalent geometry : angle 0.48104 (15233) *********************** 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: 13 poor density : 126 time to evaluate : 1.157 Fit side-chains REVERT: A 71 MET cc_start: 0.8374 (mmp) cc_final: 0.8148 (mmt) REVERT: A 227 MET cc_start: 0.8388 (mmm) cc_final: 0.8048 (mmm) REVERT: A 383 MET cc_start: 0.8707 (tpp) cc_final: 0.8389 (tpt) REVERT: C 1 MET cc_start: 0.4262 (mmt) cc_final: 0.4050 (mmm) outliers start: 13 outliers final: 10 residues processed: 135 average time/residue: 0.2316 time to fit residues: 46.2138 Evaluate side-chains 129 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 74 optimal weight: 0.3980 chunk 84 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 61 optimal weight: 20.0000 chunk 69 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3624 r_free = 0.3624 target = 0.143811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.117639 restraints weight = 13519.284| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.30 r_work: 0.3120 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1321 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= 0.107 Angle : 0.478 6.876 15233 Z= 0.242 Chirality : 0.038 0.142 1814 Planarity : 0.003 0.054 1912 Dihedral : 9.962 59.800 1717 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.58 % Allowed : 10.04 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.22), residues: 1441 helix: 1.79 (0.18), residues: 862 sheet: -0.43 (0.63), residues: 73 loop : -0.88 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 71 HIS 0.004 0.001 HIS A 451 PHE 0.009 0.001 PHE A 527 TYR 0.017 0.001 TYR A 381 ARG 0.002 0.000 ARG B 363 Details of bonding type rmsd hydrogen bonds : bond 0.03288 ( 664) hydrogen bonds : angle 4.08145 ( 1965) covalent geometry : bond 0.00243 (11226) covalent geometry : angle 0.47782 (15233) *********************** 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 141 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 1.148 Fit side-chains REVERT: A 71 MET cc_start: 0.8471 (mmp) cc_final: 0.8232 (mmt) REVERT: A 227 MET cc_start: 0.8471 (mmm) cc_final: 0.8141 (mmm) REVERT: A 383 MET cc_start: 0.8755 (tpp) cc_final: 0.8451 (tpt) REVERT: A 439 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.8329 (t0) REVERT: C 1 MET cc_start: 0.4286 (mmt) cc_final: 0.4067 (mmm) REVERT: B 93 GLN cc_start: 0.6832 (OUTLIER) cc_final: 0.6328 (pm20) outliers start: 18 outliers final: 14 residues processed: 133 average time/residue: 0.2155 time to fit residues: 42.5140 Evaluate side-chains 135 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 1.264 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 0.7980 chunk 78 optimal weight: 9.9990 chunk 92 optimal weight: 0.0670 chunk 56 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 120 optimal weight: 0.4980 chunk 9 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 = 0.3631 r_free = 0.3631 target = 0.144220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.117213 restraints weight = 13505.784| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.14 r_work: 0.3097 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1429 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= 0.099 Angle : 0.470 6.827 15233 Z= 0.237 Chirality : 0.038 0.132 1814 Planarity : 0.003 0.049 1912 Dihedral : 9.543 59.588 1717 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.50 % Allowed : 11.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.22), residues: 1441 helix: 1.97 (0.18), residues: 857 sheet: -0.36 (0.63), residues: 73 loop : -0.84 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 71 HIS 0.003 0.000 HIS A 451 PHE 0.009 0.001 PHE A 527 TYR 0.016 0.001 TYR A 381 ARG 0.002 0.000 ARG C 50 Details of bonding type rmsd hydrogen bonds : bond 0.03160 ( 664) hydrogen bonds : angle 4.00312 ( 1965) covalent geometry : bond 0.00220 (11226) covalent geometry : angle 0.47037 (15233) *********************** 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 142 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 1.209 Fit side-chains REVERT: A 227 MET cc_start: 0.8382 (mmm) cc_final: 0.8068 (mmm) REVERT: A 383 MET cc_start: 0.8675 (tpp) cc_final: 0.8393 (tpt) REVERT: A 439 ASP cc_start: 0.8603 (OUTLIER) cc_final: 0.8257 (t0) REVERT: B 93 GLN cc_start: 0.6853 (OUTLIER) cc_final: 0.6175 (pm20) outliers start: 17 outliers final: 12 residues processed: 136 average time/residue: 0.2086 time to fit residues: 42.4751 Evaluate side-chains 136 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 1.129 ------------------------------------------------------------------------------- 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 439 ASP Chi-restraints excluded: chain C residue 157 GLN Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 93 GLN 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 134 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 81 optimal weight: 0.0980 chunk 97 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3607 r_free = 0.3607 target = 0.142462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.114236 restraints weight = 13644.363| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.25 r_work: 0.3058 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11226 Z= 0.109 Angle : 0.478 6.786 15233 Z= 0.242 Chirality : 0.039 0.207 1814 Planarity : 0.003 0.048 1912 Dihedral : 9.313 58.891 1717 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.11 % Allowed : 11.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.22), residues: 1441 helix: 1.95 (0.18), residues: 865 sheet: -0.29 (0.64), residues: 73 loop : -0.89 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 71 HIS 0.004 0.001 HIS A 451 PHE 0.009 0.001 PHE A 527 TYR 0.017 0.001 TYR A 381 ARG 0.002 0.000 ARG C 50 Details of bonding type rmsd hydrogen bonds : bond 0.03228 ( 664) hydrogen bonds : angle 4.00248 ( 1965) covalent geometry : bond 0.00251 (11226) covalent geometry : angle 0.47813 (15233) *********************** 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 148 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 1.143 Fit side-chains REVERT: A 44 ARG cc_start: 0.8159 (ttt180) cc_final: 0.7891 (ptm-80) REVERT: A 227 MET cc_start: 0.8432 (mmm) cc_final: 0.8122 (mmm) REVERT: A 383 MET cc_start: 0.8673 (tpp) cc_final: 0.8412 (tpt) REVERT: A 439 ASP cc_start: 0.8653 (OUTLIER) cc_final: 0.8333 (t0) REVERT: B 93 GLN cc_start: 0.6772 (OUTLIER) cc_final: 0.5985 (pm20) REVERT: B 403 ARG cc_start: 0.6675 (tpp80) cc_final: 0.6403 (ttp-170) outliers start: 24 outliers final: 17 residues processed: 139 average time/residue: 0.2180 time to fit residues: 44.8764 Evaluate side-chains 140 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 1.167 ------------------------------------------------------------------------------- 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 19 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 184 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 57 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 130 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 390 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.140850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.111470 restraints weight = 13723.669| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.26 r_work: 0.3022 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1709 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= 0.119 Angle : 0.486 6.806 15233 Z= 0.246 Chirality : 0.039 0.133 1814 Planarity : 0.003 0.045 1912 Dihedral : 9.131 58.404 1717 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.11 % Allowed : 12.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.22), residues: 1441 helix: 1.92 (0.18), residues: 864 sheet: -0.30 (0.64), residues: 73 loop : -0.79 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 71 HIS 0.005 0.001 HIS A 451 PHE 0.009 0.001 PHE A 527 TYR 0.019 0.001 TYR A 381 ARG 0.002 0.000 ARG A 157 Details of bonding type rmsd hydrogen bonds : bond 0.03342 ( 664) hydrogen bonds : angle 4.05064 ( 1965) covalent geometry : bond 0.00277 (11226) covalent geometry : angle 0.48560 (15233) *********************** 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 142 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 1.159 Fit side-chains REVERT: A 44 ARG cc_start: 0.8176 (ttt180) cc_final: 0.7917 (ptm-80) REVERT: A 227 MET cc_start: 0.8505 (mmm) cc_final: 0.8200 (mmm) REVERT: A 287 MET cc_start: 0.8786 (mtt) cc_final: 0.8535 (mtt) REVERT: A 383 MET cc_start: 0.8699 (tpp) cc_final: 0.8402 (tpt) REVERT: A 439 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8270 (t0) REVERT: B 93 GLN cc_start: 0.6760 (OUTLIER) cc_final: 0.5829 (pm20) REVERT: B 213 ARG cc_start: 0.6645 (tpm170) cc_final: 0.6251 (tpp-160) REVERT: B 360 PHE cc_start: 0.5815 (t80) cc_final: 0.5577 (t80) REVERT: B 403 ARG cc_start: 0.6792 (tpp80) cc_final: 0.6381 (mtm180) outliers start: 24 outliers final: 17 residues processed: 133 average time/residue: 0.2305 time to fit residues: 44.8637 Evaluate side-chains 134 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 1.161 ------------------------------------------------------------------------------- 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 19 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 184 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 83 optimal weight: 2.9990 chunk 113 optimal weight: 0.0370 chunk 69 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.7458 ------------------------------------------------------------------------------- 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 = 0.3602 r_free = 0.3602 target = 0.141929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.114745 restraints weight = 13535.135| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.13 r_work: 0.3052 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11226 Z= 0.109 Angle : 0.476 6.797 15233 Z= 0.241 Chirality : 0.038 0.133 1814 Planarity : 0.003 0.044 1912 Dihedral : 9.025 59.682 1717 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.02 % Allowed : 12.32 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.22), residues: 1441 helix: 1.99 (0.18), residues: 865 sheet: -0.33 (0.64), residues: 73 loop : -0.79 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 71 HIS 0.005 0.001 HIS A 451 PHE 0.009 0.001 PHE A 527 TYR 0.017 0.001 TYR A 381 ARG 0.001 0.000 ARG B 403 Details of bonding type rmsd hydrogen bonds : bond 0.03250 ( 664) hydrogen bonds : angle 4.02364 ( 1965) covalent geometry : bond 0.00250 (11226) covalent geometry : angle 0.47617 (15233) *********************** 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 139 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 1.025 Fit side-chains REVERT: A 44 ARG cc_start: 0.8187 (ttt180) cc_final: 0.7954 (ptm-80) REVERT: A 227 MET cc_start: 0.8472 (mmm) cc_final: 0.8170 (mmm) REVERT: A 287 MET cc_start: 0.8793 (mtt) cc_final: 0.8535 (mtt) REVERT: A 383 MET cc_start: 0.8698 (tpp) cc_final: 0.8392 (tpt) REVERT: A 439 ASP cc_start: 0.8555 (OUTLIER) cc_final: 0.8275 (t0) REVERT: B 93 GLN cc_start: 0.6733 (OUTLIER) cc_final: 0.5789 (pm20) REVERT: B 213 ARG cc_start: 0.6678 (tpm170) cc_final: 0.6293 (tpp-160) REVERT: B 360 PHE cc_start: 0.5803 (t80) cc_final: 0.5583 (t80) outliers start: 23 outliers final: 18 residues processed: 132 average time/residue: 0.3030 time to fit residues: 61.5867 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 : 2.069 ------------------------------------------------------------------------------- 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 188 VAL Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 354 ILE 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 33 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 139 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.140892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.113907 restraints weight = 13769.740| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.21 r_work: 0.3034 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11226 Z= 0.112 Angle : 0.482 6.790 15233 Z= 0.244 Chirality : 0.038 0.133 1814 Planarity : 0.003 0.043 1912 Dihedral : 8.900 59.931 1717 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.85 % Allowed : 12.50 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.22), residues: 1441 helix: 2.00 (0.18), residues: 865 sheet: -0.43 (0.64), residues: 75 loop : -0.75 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 115 HIS 0.005 0.001 HIS A 451 PHE 0.008 0.001 PHE A 527 TYR 0.017 0.001 TYR A 381 ARG 0.001 0.000 ARG B 402 Details of bonding type rmsd hydrogen bonds : bond 0.03250 ( 664) hydrogen bonds : angle 4.02181 ( 1965) covalent geometry : bond 0.00260 (11226) covalent geometry : angle 0.48232 (15233) *********************** 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: 21 poor density : 115 time to evaluate : 1.282 Fit side-chains REVERT: A 44 ARG cc_start: 0.8153 (ttt180) cc_final: 0.7908 (ptm-80) REVERT: A 227 MET cc_start: 0.8503 (mmm) cc_final: 0.8200 (mmm) REVERT: A 287 MET cc_start: 0.8764 (mtt) cc_final: 0.8511 (mtt) REVERT: A 383 MET cc_start: 0.8681 (tpp) cc_final: 0.8383 (tpt) REVERT: A 439 ASP cc_start: 0.8564 (OUTLIER) cc_final: 0.8296 (t0) REVERT: B 93 GLN cc_start: 0.6752 (OUTLIER) cc_final: 0.5811 (pm20) REVERT: B 213 ARG cc_start: 0.6672 (tpm170) cc_final: 0.6260 (tpp-160) REVERT: B 360 PHE cc_start: 0.5829 (t80) cc_final: 0.5602 (t80) REVERT: B 403 ARG cc_start: 0.6817 (tpp80) cc_final: 0.6379 (ttp-170) outliers start: 21 outliers final: 18 residues processed: 129 average time/residue: 0.2365 time to fit residues: 44.9906 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 : 1.334 ------------------------------------------------------------------------------- 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 188 VAL Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 354 ILE 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 60 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 1 optimal weight: 0.0980 chunk 12 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 106 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.140204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.111748 restraints weight = 13675.723| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.26 r_work: 0.3035 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11226 Z= 0.120 Angle : 0.490 6.791 15233 Z= 0.249 Chirality : 0.039 0.133 1814 Planarity : 0.003 0.043 1912 Dihedral : 8.831 59.688 1717 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.76 % Allowed : 12.68 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.22), residues: 1441 helix: 1.97 (0.18), residues: 864 sheet: -0.44 (0.64), residues: 75 loop : -0.70 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 71 HIS 0.005 0.001 HIS A 451 PHE 0.008 0.001 PHE A 527 TYR 0.018 0.001 TYR A 381 ARG 0.001 0.000 ARG B 403 Details of bonding type rmsd hydrogen bonds : bond 0.03331 ( 664) hydrogen bonds : angle 4.05030 ( 1965) covalent geometry : bond 0.00281 (11226) covalent geometry : angle 0.48988 (15233) ********************** 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 139 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 1.230 Fit side-chains REVERT: A 44 ARG cc_start: 0.8178 (ttt180) cc_final: 0.7925 (ptm-80) REVERT: A 227 MET cc_start: 0.8511 (mmm) cc_final: 0.8206 (mmm) REVERT: A 287 MET cc_start: 0.8783 (mtt) cc_final: 0.8535 (mtt) REVERT: A 383 MET cc_start: 0.8686 (tpp) cc_final: 0.8389 (tpt) REVERT: A 439 ASP cc_start: 0.8546 (OUTLIER) cc_final: 0.8275 (t0) REVERT: B 93 GLN cc_start: 0.6803 (OUTLIER) cc_final: 0.5821 (pm20) REVERT: B 213 ARG cc_start: 0.6707 (tpm170) cc_final: 0.6273 (tpp-160) REVERT: B 360 PHE cc_start: 0.5881 (t80) cc_final: 0.5612 (t80) REVERT: B 403 ARG cc_start: 0.6809 (tpp80) cc_final: 0.6187 (mtm180) outliers start: 20 outliers final: 18 residues processed: 132 average time/residue: 0.2253 time to fit residues: 43.4034 Evaluate side-chains 137 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 1.140 ------------------------------------------------------------------------------- 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 188 VAL Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 354 ILE 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 110 optimal weight: 0.7980 chunk 141 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 90 optimal weight: 0.0770 chunk 119 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- 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 = 0.3592 r_free = 0.3592 target = 0.141054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.113645 restraints weight = 13582.140| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.13 r_work: 0.3042 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11226 Z= 0.111 Angle : 0.483 6.780 15233 Z= 0.245 Chirality : 0.038 0.133 1814 Planarity : 0.003 0.043 1912 Dihedral : 8.733 59.298 1717 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.02 % Allowed : 12.41 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.22), residues: 1441 helix: 2.00 (0.18), residues: 865 sheet: -0.40 (0.65), residues: 75 loop : -0.73 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 115 HIS 0.004 0.001 HIS A 451 PHE 0.008 0.001 PHE A 527 TYR 0.017 0.001 TYR A 381 ARG 0.001 0.000 ARG B 403 Details of bonding type rmsd hydrogen bonds : bond 0.03240 ( 664) hydrogen bonds : angle 4.02259 ( 1965) covalent geometry : bond 0.00256 (11226) covalent geometry : angle 0.48300 (15233) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5633.33 seconds wall clock time: 99 minutes 16.66 seconds (5956.66 seconds total)