Starting phenix.real_space_refine on Wed Mar 12 09:27:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7b5s_12050/03_2025/7b5s_12050.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b5s_12050/03_2025/7b5s_12050.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7b5s_12050/03_2025/7b5s_12050.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b5s_12050/03_2025/7b5s_12050.map" model { file = "/net/cci-nas-00/data/ceres_data/7b5s_12050/03_2025/7b5s_12050.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b5s_12050/03_2025/7b5s_12050.cif" } resolution = 3.6 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 5 6.06 5 S 51 5.16 5 C 4876 2.51 5 N 1328 2.21 5 O 1411 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7671 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 5157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 5157 Classifications: {'peptide': 634} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 10, 'TRANS': 623} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "H" Number of atoms: 1832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1832 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 210} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "R" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 677 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5289 SG CYS H 276 74.246 18.842 51.812 1.00117.24 S ATOM 5322 SG CYS H 281 72.428 16.447 54.367 1.00135.41 S ATOM 5453 SG CYS H 297 70.707 18.082 51.435 1.00131.43 S ATOM 5468 SG CYS H 299 71.810 20.100 54.558 1.00133.40 S ATOM 5509 SG CYS H 304 76.310 26.245 41.910 1.00100.27 S ATOM 5534 SG CYS H 307 79.658 25.355 41.531 1.00 95.27 S ATOM 5616 SG CYS H 317 78.195 27.306 38.568 1.00 70.99 S ATOM 7177 SG CYS R 42 69.077 57.905 32.569 1.00 46.85 S ATOM 7196 SG CYS R 45 69.268 56.455 36.282 1.00 43.75 S ATOM 7444 SG CYS R 83 71.090 59.547 35.358 1.00 53.09 S ATOM 7373 SG CYS R 75 73.529 60.384 19.938 1.00 75.14 S ATOM 7540 SG CYS R 94 75.023 58.860 23.232 1.00 70.69 S ATOM 7263 SG CYS R 53 69.020 61.737 39.490 1.00 58.47 S ATOM 7286 SG CYS R 56 67.332 64.720 41.123 1.00 61.71 S ATOM 7323 SG CYS R 68 66.372 63.491 37.491 1.00 65.60 S Time building chain proxies: 5.32, per 1000 atoms: 0.69 Number of scatterers: 7671 At special positions: 0 Unit cell: (111.18, 93.74, 163.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 5 29.99 S 51 16.00 O 1411 8.00 N 1328 7.00 C 4876 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: 1.74 Conformation dependent library (CDL) restraints added in 938.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H 601 " pdb="ZN ZN H 601 " - pdb=" SG CYS H 297 " pdb="ZN ZN H 601 " - pdb=" SG CYS H 281 " pdb="ZN ZN H 601 " - pdb=" SG CYS H 299 " pdb="ZN ZN H 601 " - pdb=" SG CYS H 276 " pdb=" ZN H 602 " pdb="ZN ZN H 602 " - pdb=" NE2 HIS H 312 " pdb="ZN ZN H 602 " - pdb=" SG CYS H 307 " pdb="ZN ZN H 602 " - pdb=" SG CYS H 304 " pdb="ZN ZN H 602 " - pdb=" SG CYS H 317 " pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 80 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 42 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 45 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 83 " pdb=" ZN R 202 " pdb="ZN ZN R 202 " - pdb=" ND1 HIS R 77 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 75 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 94 " pdb=" ZN R 203 " pdb="ZN ZN R 203 " - pdb=" ND1 HIS R 82 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 53 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 68 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 56 " Number of angles added : 15 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1808 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 6 sheets defined 64.9% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'C' and resid 20 through 32 Processing helix chain 'C' and resid 38 through 53 removed outlier: 3.624A pdb=" N TYR C 42 " --> pdb=" O ALA C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 105 Processing helix chain 'C' and resid 114 through 137 removed outlier: 3.843A pdb=" N GLN C 121 " --> pdb=" O LYS C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 144 removed outlier: 3.566A pdb=" N HIS C 143 " --> pdb=" O TYR C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 172 Processing helix chain 'C' and resid 174 through 188 Processing helix chain 'C' and resid 189 through 191 No H-bonds generated for 'chain 'C' and resid 189 through 191' Processing helix chain 'C' and resid 198 through 211 removed outlier: 3.904A pdb=" N GLY C 203 " --> pdb=" O ARG C 199 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N VAL C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 232 Processing helix chain 'C' and resid 232 through 253 removed outlier: 3.781A pdb=" N THR C 249 " --> pdb=" O THR C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 275 removed outlier: 3.730A pdb=" N TYR C 260 " --> pdb=" O PRO C 256 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL C 275 " --> pdb=" O GLU C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 295 Processing helix chain 'C' and resid 299 through 313 Processing helix chain 'C' and resid 317 through 328 removed outlier: 3.877A pdb=" N ARG C 321 " --> pdb=" O GLU C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 354 removed outlier: 3.857A pdb=" N LYS C 338 " --> pdb=" O GLY C 334 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 361 removed outlier: 3.584A pdb=" N ALA C 359 " --> pdb=" O GLY C 356 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASN C 361 " --> pdb=" O ALA C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 384 removed outlier: 3.602A pdb=" N TYR C 366 " --> pdb=" O ASP C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 405 removed outlier: 3.508A pdb=" N ASN C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 412 Processing helix chain 'C' and resid 417 through 431 Processing helix chain 'C' and resid 438 through 455 Processing helix chain 'C' and resid 458 through 476 removed outlier: 4.016A pdb=" N PHE C 462 " --> pdb=" O ASP C 458 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN C 463 " --> pdb=" O LYS C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 497 Processing helix chain 'C' and resid 501 through 525 removed outlier: 3.558A pdb=" N GLN C 505 " --> pdb=" O THR C 501 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE C 511 " --> pdb=" O MET C 507 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU C 519 " --> pdb=" O LYS C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 528 No H-bonds generated for 'chain 'C' and resid 526 through 528' Processing helix chain 'C' and resid 559 through 574 removed outlier: 3.628A pdb=" N ARG C 573 " --> pdb=" O PHE C 569 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N HIS C 574 " --> pdb=" O TYR C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 613 Processing helix chain 'C' and resid 622 through 630 removed outlier: 3.765A pdb=" N SER C 628 " --> pdb=" O GLN C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 646 Processing helix chain 'H' and resid 316 through 326 removed outlier: 4.237A pdb=" N LYS H 326 " --> pdb=" O LYS H 322 " (cutoff:3.500A) Processing helix chain 'H' and resid 408 through 430 removed outlier: 3.641A pdb=" N GLN H 412 " --> pdb=" O ARG H 408 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE H 430 " --> pdb=" O GLN H 426 " (cutoff:3.500A) Processing helix chain 'H' and resid 430 through 448 removed outlier: 3.625A pdb=" N HIS H 448 " --> pdb=" O GLU H 444 " (cutoff:3.500A) Processing helix chain 'H' and resid 452 through 481 removed outlier: 3.986A pdb=" N TYR H 474 " --> pdb=" O ALA H 470 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL H 477 " --> pdb=" O MET H 473 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR H 481 " --> pdb=" O VAL H 477 " (cutoff:3.500A) Processing helix chain 'H' and resid 485 through 513 removed outlier: 3.652A pdb=" N ILE H 490 " --> pdb=" O ASN H 486 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE H 491 " --> pdb=" O GLN H 487 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA H 496 " --> pdb=" O GLU H 492 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP H 497 " --> pdb=" O ASN H 493 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU H 510 " --> pdb=" O SER H 506 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG H 511 " --> pdb=" O GLY H 507 " (cutoff:3.500A) Processing helix chain 'H' and resid 517 through 550 removed outlier: 4.251A pdb=" N GLN H 523 " --> pdb=" O GLN H 519 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR H 531 " --> pdb=" O ASP H 527 " (cutoff:3.500A) Processing helix chain 'R' and resid 53 through 58 removed outlier: 4.046A pdb=" N ALA R 58 " --> pdb=" O ILE R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 91 removed outlier: 4.162A pdb=" N ARG R 86 " --> pdb=" O HIS R 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 534 through 540 removed outlier: 5.931A pdb=" N ASP C 534 " --> pdb=" O TRP R 27 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ALA R 29 " --> pdb=" O ASP C 534 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N SER C 536 " --> pdb=" O ALA R 29 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N ALA R 31 " --> pdb=" O SER C 536 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLN C 538 " --> pdb=" O ALA R 31 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS R 26 " --> pdb=" O GLU C 589 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS C 587 " --> pdb=" O ASN R 28 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N VAL R 30 " --> pdb=" O LEU C 585 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU C 585 " --> pdb=" O VAL R 30 " (cutoff:3.500A) removed outlier: 11.594A pdb=" N LEU R 32 " --> pdb=" O TYR C 583 " (cutoff:3.500A) removed outlier: 10.888A pdb=" N TYR C 583 " --> pdb=" O LEU R 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 601 through 602 Processing sheet with id=AA3, first strand: chain 'C' and resid 619 through 621 removed outlier: 3.885A pdb=" N TYR C 620 " --> pdb=" O ILE C 669 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 101 through 104 Processing sheet with id=AA5, first strand: chain 'H' and resid 294 through 296 Processing sheet with id=AA6, first strand: chain 'R' and resid 70 through 72 removed outlier: 3.507A pdb=" N PHE R 79 " --> pdb=" O ALA R 71 " (cutoff:3.500A) 430 hydrogen bonds defined for protein. 1281 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.07 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2499 1.34 - 1.46: 1858 1.46 - 1.59: 3391 1.59 - 1.71: 0 1.71 - 1.83: 72 Bond restraints: 7820 Sorted by residual: bond pdb=" N VAL H 504 " pdb=" CA VAL H 504 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 7.85e+00 bond pdb=" N ILE H 521 " pdb=" CA ILE H 521 " ideal model delta sigma weight residual 1.461 1.490 -0.030 1.19e-02 7.06e+03 6.23e+00 bond pdb=" N LEU H 505 " pdb=" CA LEU H 505 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.19e-02 7.06e+03 5.62e+00 bond pdb=" N LYS H 522 " pdb=" CA LYS H 522 " ideal model delta sigma weight residual 1.459 1.486 -0.026 1.19e-02 7.06e+03 4.87e+00 bond pdb=" CA GLN H 487 " pdb=" C GLN H 487 " ideal model delta sigma weight residual 1.522 1.503 0.020 1.37e-02 5.33e+03 2.10e+00 ... (remaining 7815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 10294 2.16 - 4.32: 210 4.32 - 6.49: 32 6.49 - 8.65: 3 8.65 - 10.81: 3 Bond angle restraints: 10542 Sorted by residual: angle pdb=" N VAL C 145 " pdb=" CA VAL C 145 " pdb=" C VAL C 145 " ideal model delta sigma weight residual 112.83 107.90 4.93 9.90e-01 1.02e+00 2.48e+01 angle pdb=" N ILE H 521 " pdb=" CA ILE H 521 " pdb=" C ILE H 521 " ideal model delta sigma weight residual 110.62 105.69 4.93 1.02e+00 9.61e-01 2.34e+01 angle pdb=" CA PRO H 277 " pdb=" N PRO H 277 " pdb=" CD PRO H 277 " ideal model delta sigma weight residual 112.00 105.98 6.02 1.40e+00 5.10e-01 1.85e+01 angle pdb=" N MET C 111 " pdb=" CA MET C 111 " pdb=" CB MET C 111 " ideal model delta sigma weight residual 114.17 109.44 4.73 1.14e+00 7.69e-01 1.72e+01 angle pdb=" N TRP C 144 " pdb=" CA TRP C 144 " pdb=" C TRP C 144 " ideal model delta sigma weight residual 114.56 109.77 4.79 1.27e+00 6.20e-01 1.42e+01 ... (remaining 10537 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4163 17.94 - 35.88: 472 35.88 - 53.81: 70 53.81 - 71.75: 15 71.75 - 89.69: 9 Dihedral angle restraints: 4729 sinusoidal: 1950 harmonic: 2779 Sorted by residual: dihedral pdb=" CA ASP C 217 " pdb=" C ASP C 217 " pdb=" N ALA C 218 " pdb=" CA ALA C 218 " ideal model delta harmonic sigma weight residual 180.00 154.72 25.28 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA LEU C 110 " pdb=" C LEU C 110 " pdb=" N MET C 111 " pdb=" CA MET C 111 " ideal model delta harmonic sigma weight residual 180.00 158.25 21.75 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA PRO C 530 " pdb=" C PRO C 530 " pdb=" N LEU C 531 " pdb=" CA LEU C 531 " ideal model delta harmonic sigma weight residual -180.00 -159.21 -20.79 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 4726 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 949 0.057 - 0.113: 171 0.113 - 0.170: 18 0.170 - 0.227: 3 0.227 - 0.283: 1 Chirality restraints: 1142 Sorted by residual: chirality pdb=" CA ILE H 521 " pdb=" N ILE H 521 " pdb=" C ILE H 521 " pdb=" CB ILE H 521 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CB THR C 580 " pdb=" CA THR C 580 " pdb=" OG1 THR C 580 " pdb=" CG2 THR C 580 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB ILE H 513 " pdb=" CA ILE H 513 " pdb=" CG1 ILE H 513 " pdb=" CG2 ILE H 513 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.38e-01 ... (remaining 1139 not shown) Planarity restraints: 1342 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS H 276 " -0.103 5.00e-02 4.00e+02 1.54e-01 3.78e+01 pdb=" N PRO H 277 " 0.266 5.00e-02 4.00e+02 pdb=" CA PRO H 277 " -0.086 5.00e-02 4.00e+02 pdb=" CD PRO H 277 " -0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 173 " -0.041 5.00e-02 4.00e+02 6.13e-02 6.00e+00 pdb=" N PRO C 174 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO C 174 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 174 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU H 509 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.40e+00 pdb=" C LEU H 509 " -0.032 2.00e-02 2.50e+03 pdb=" O LEU H 509 " 0.012 2.00e-02 2.50e+03 pdb=" N GLU H 510 " 0.011 2.00e-02 2.50e+03 ... (remaining 1339 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 70 2.58 - 3.16: 6525 3.16 - 3.74: 11264 3.74 - 4.32: 14710 4.32 - 4.90: 24744 Nonbonded interactions: 57313 Sorted by model distance: nonbonded pdb=" OD2 ASP R 97 " pdb="ZN ZN R 202 " model vdw 1.997 2.230 nonbonded pdb=" O LYS C 459 " pdb=" OH TYR C 500 " model vdw 2.130 3.040 nonbonded pdb=" N GLU H 454 " pdb=" OE1 GLU H 454 " model vdw 2.191 3.120 nonbonded pdb=" OH TYR C 244 " pdb=" OE2 GLU C 271 " model vdw 2.200 3.040 nonbonded pdb=" OH TYR C 260 " pdb=" O LEU C 295 " model vdw 2.222 3.040 ... (remaining 57308 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.460 Find NCS groups from input model: 0.090 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:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 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 : 0.006 0.045 7820 Z= 0.397 Angle : 0.783 10.810 10542 Z= 0.459 Chirality : 0.045 0.283 1142 Planarity : 0.005 0.154 1342 Dihedral : 15.477 89.688 2921 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 0.24 % Allowed : 0.24 % Favored : 99.52 % 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: -0.49 (0.28), residues: 915 helix: 1.05 (0.22), residues: 546 sheet: 0.79 (1.67), residues: 10 loop : -2.66 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 33 HIS 0.003 0.001 HIS C 343 PHE 0.020 0.002 PHE C 303 TYR 0.021 0.002 TYR C 377 ARG 0.006 0.001 ARG H 511 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: C 143 HIS cc_start: 0.7798 (m-70) cc_final: 0.7366 (m90) REVERT: C 672 TYR cc_start: 0.8488 (t80) cc_final: 0.8021 (t80) REVERT: H 521 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.8071 (mt) REVERT: R 54 ILE cc_start: 0.9197 (tp) cc_final: 0.8770 (tp) outliers start: 2 outliers final: 0 residues processed: 105 average time/residue: 0.1879 time to fit residues: 27.5243 Evaluate side-chains 86 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 521 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.7980 chunk 69 optimal weight: 0.0370 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 53 optimal weight: 0.4980 chunk 83 optimal weight: 0.5980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 304 HIS ** C 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.138813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.103443 restraints weight = 12467.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.106206 restraints weight = 8109.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.108122 restraints weight = 6111.704| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7820 Z= 0.190 Angle : 0.574 8.771 10542 Z= 0.309 Chirality : 0.038 0.207 1142 Planarity : 0.004 0.096 1342 Dihedral : 4.699 23.058 1023 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 1.08 % Allowed : 8.15 % Favored : 90.77 % 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: 0.21 (0.29), residues: 915 helix: 1.59 (0.22), residues: 564 sheet: 1.54 (1.84), residues: 10 loop : -2.56 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 452 HIS 0.005 0.001 HIS C 345 PHE 0.029 0.001 PHE H 457 TYR 0.024 0.001 TYR H 529 ARG 0.004 0.000 ARG H 511 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.813 Fit side-chains revert: symmetry clash REVERT: C 90 LYS cc_start: 0.8693 (tppt) cc_final: 0.8039 (tttm) REVERT: C 143 HIS cc_start: 0.8074 (m-70) cc_final: 0.7690 (m90) REVERT: C 488 MET cc_start: 0.8632 (tpt) cc_final: 0.8255 (tpt) REVERT: C 589 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6807 (mm-30) REVERT: H 275 TRP cc_start: 0.7233 (m100) cc_final: 0.7008 (m100) REVERT: H 497 ASP cc_start: 0.7726 (t0) cc_final: 0.7450 (t0) REVERT: R 54 ILE cc_start: 0.9075 (tp) cc_final: 0.8725 (tp) outliers start: 9 outliers final: 7 residues processed: 110 average time/residue: 0.1755 time to fit residues: 27.2287 Evaluate side-chains 93 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain H residue 273 LEU Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 93 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 32 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 30 optimal weight: 0.0980 chunk 63 optimal weight: 0.0980 chunk 14 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 40 optimal weight: 0.3980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 607 GLN ** 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 = 0.3744 r_free = 0.3744 target = 0.141911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.106869 restraints weight = 12242.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.109479 restraints weight = 8287.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.111184 restraints weight = 6406.127| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7820 Z= 0.170 Angle : 0.533 6.817 10542 Z= 0.287 Chirality : 0.037 0.163 1142 Planarity : 0.004 0.076 1342 Dihedral : 4.502 23.311 1021 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 1.44 % Allowed : 10.91 % Favored : 87.65 % 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: 0.47 (0.29), residues: 915 helix: 1.83 (0.22), residues: 567 sheet: 1.60 (1.84), residues: 10 loop : -2.57 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 167 HIS 0.004 0.001 HIS C 345 PHE 0.021 0.001 PHE H 457 TYR 0.022 0.001 TYR H 529 ARG 0.002 0.000 ARG C 173 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.886 Fit side-chains revert: symmetry clash REVERT: C 90 LYS cc_start: 0.8619 (tppt) cc_final: 0.7934 (tttm) REVERT: C 143 HIS cc_start: 0.7958 (m-70) cc_final: 0.7548 (m90) REVERT: C 427 ASP cc_start: 0.8165 (t0) cc_final: 0.7954 (t0) REVERT: C 589 GLU cc_start: 0.7080 (mm-30) cc_final: 0.6805 (mm-30) REVERT: C 620 TYR cc_start: 0.7420 (m-80) cc_final: 0.6942 (m-80) REVERT: C 681 ARG cc_start: 0.7861 (ttm-80) cc_final: 0.7584 (ttm-80) REVERT: H 450 MET cc_start: 0.4389 (mmm) cc_final: 0.4132 (mmt) REVERT: H 458 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7975 (mp) REVERT: H 473 MET cc_start: 0.7974 (tpp) cc_final: 0.7318 (tpp) REVERT: H 497 ASP cc_start: 0.7786 (t0) cc_final: 0.7505 (t0) REVERT: H 499 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7393 (tt0) REVERT: R 54 ILE cc_start: 0.9077 (tp) cc_final: 0.8749 (tp) outliers start: 12 outliers final: 7 residues processed: 103 average time/residue: 0.1764 time to fit residues: 25.7693 Evaluate side-chains 97 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain H residue 273 LEU Chi-restraints excluded: chain H residue 458 LEU Chi-restraints excluded: chain H residue 499 GLU Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 93 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 63 optimal weight: 0.2980 chunk 85 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 71 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 59 optimal weight: 0.1980 chunk 65 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 607 GLN ** 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 = 0.3735 r_free = 0.3735 target = 0.141085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.105594 restraints weight = 12116.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.108242 restraints weight = 8229.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.109982 restraints weight = 6368.220| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7820 Z= 0.188 Angle : 0.528 9.052 10542 Z= 0.285 Chirality : 0.037 0.169 1142 Planarity : 0.004 0.065 1342 Dihedral : 4.406 22.829 1021 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 2.28 % Allowed : 13.43 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.61 (0.29), residues: 915 helix: 1.96 (0.22), residues: 567 sheet: 1.53 (1.85), residues: 10 loop : -2.53 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 452 HIS 0.003 0.001 HIS C 345 PHE 0.021 0.001 PHE H 457 TYR 0.022 0.001 TYR H 529 ARG 0.002 0.000 ARG H 511 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: C 90 LYS cc_start: 0.8578 (tppt) cc_final: 0.7898 (tttm) REVERT: C 143 HIS cc_start: 0.8004 (m-70) cc_final: 0.7767 (m-70) REVERT: C 589 GLU cc_start: 0.6972 (mm-30) cc_final: 0.6688 (mm-30) REVERT: C 620 TYR cc_start: 0.7448 (m-80) cc_final: 0.6867 (m-80) REVERT: C 681 ARG cc_start: 0.7808 (ttm-80) cc_final: 0.7460 (ttm-80) REVERT: H 449 ASN cc_start: 0.6766 (p0) cc_final: 0.6475 (p0) REVERT: H 455 VAL cc_start: 0.6267 (OUTLIER) cc_final: 0.6044 (m) REVERT: H 458 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7901 (mp) REVERT: H 473 MET cc_start: 0.7953 (tpp) cc_final: 0.7197 (tpp) REVERT: H 497 ASP cc_start: 0.7935 (t0) cc_final: 0.7631 (t0) REVERT: H 499 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7396 (tt0) REVERT: R 50 MET cc_start: 0.8608 (mmm) cc_final: 0.8272 (mmm) REVERT: R 54 ILE cc_start: 0.9095 (tp) cc_final: 0.8814 (tp) outliers start: 19 outliers final: 13 residues processed: 106 average time/residue: 0.1802 time to fit residues: 27.1707 Evaluate side-chains 106 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain H residue 273 LEU Chi-restraints excluded: chain H residue 427 SER Chi-restraints excluded: chain H residue 443 GLU Chi-restraints excluded: chain H residue 455 VAL Chi-restraints excluded: chain H residue 458 LEU Chi-restraints excluded: chain H residue 499 GLU Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 93 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 71 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 30 optimal weight: 0.1980 chunk 0 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 10 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: C 30 GLN ** C 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 519 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.139439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.103736 restraints weight = 12279.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.106267 restraints weight = 8369.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.107997 restraints weight = 6526.684| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7820 Z= 0.231 Angle : 0.548 7.544 10542 Z= 0.297 Chirality : 0.038 0.201 1142 Planarity : 0.004 0.060 1342 Dihedral : 4.447 23.609 1021 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 3.00 % Allowed : 14.63 % Favored : 82.37 % 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: 0.61 (0.29), residues: 915 helix: 1.95 (0.22), residues: 566 sheet: 1.47 (1.87), residues: 10 loop : -2.50 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 35 HIS 0.003 0.001 HIS C 345 PHE 0.023 0.001 PHE H 457 TYR 0.023 0.001 TYR H 529 ARG 0.003 0.000 ARG C 173 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.823 Fit side-chains revert: symmetry clash REVERT: C 90 LYS cc_start: 0.8625 (tppt) cc_final: 0.7931 (tttm) REVERT: C 143 HIS cc_start: 0.8106 (m-70) cc_final: 0.7663 (m90) REVERT: C 589 GLU cc_start: 0.7029 (mm-30) cc_final: 0.6742 (mm-30) REVERT: C 620 TYR cc_start: 0.7468 (m-80) cc_final: 0.6823 (m-80) REVERT: C 672 TYR cc_start: 0.8458 (t80) cc_final: 0.8146 (t80) REVERT: C 681 ARG cc_start: 0.7873 (ttm-80) cc_final: 0.7510 (ttm-80) REVERT: H 473 MET cc_start: 0.7942 (tpp) cc_final: 0.7142 (tpp) REVERT: H 497 ASP cc_start: 0.7927 (t0) cc_final: 0.7641 (t0) REVERT: H 499 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7343 (tt0) REVERT: R 54 ILE cc_start: 0.9092 (tp) cc_final: 0.8826 (tp) outliers start: 25 outliers final: 20 residues processed: 107 average time/residue: 0.1737 time to fit residues: 26.2997 Evaluate side-chains 109 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain H residue 273 LEU Chi-restraints excluded: chain H residue 427 SER Chi-restraints excluded: chain H residue 443 GLU Chi-restraints excluded: chain H residue 457 PHE Chi-restraints excluded: chain H residue 471 THR Chi-restraints excluded: chain H residue 499 GLU Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 93 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 89 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 30 optimal weight: 0.0060 chunk 10 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 519 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.139680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.104143 restraints weight = 12078.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.106692 restraints weight = 8245.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.108387 restraints weight = 6419.424| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7820 Z= 0.217 Angle : 0.542 7.754 10542 Z= 0.293 Chirality : 0.038 0.212 1142 Planarity : 0.004 0.058 1342 Dihedral : 4.408 23.555 1021 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 3.12 % Allowed : 14.75 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.67 (0.29), residues: 915 helix: 1.99 (0.22), residues: 566 sheet: 1.49 (1.87), residues: 10 loop : -2.46 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 35 HIS 0.003 0.001 HIS C 345 PHE 0.024 0.001 PHE H 457 TYR 0.023 0.001 TYR H 529 ARG 0.002 0.000 ARG H 511 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.830 Fit side-chains revert: symmetry clash REVERT: C 90 LYS cc_start: 0.8597 (tppt) cc_final: 0.8313 (mmtm) REVERT: C 143 HIS cc_start: 0.8160 (m-70) cc_final: 0.7726 (m90) REVERT: C 589 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6705 (mm-30) REVERT: C 620 TYR cc_start: 0.7481 (m-80) cc_final: 0.6788 (m-80) REVERT: C 681 ARG cc_start: 0.7978 (ttm-80) cc_final: 0.7602 (ttm-80) REVERT: H 458 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7912 (mp) REVERT: H 473 MET cc_start: 0.7952 (tpp) cc_final: 0.7164 (tpp) REVERT: H 499 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7353 (tt0) REVERT: R 50 MET cc_start: 0.8649 (mmm) cc_final: 0.8296 (mmm) REVERT: R 54 ILE cc_start: 0.9085 (tp) cc_final: 0.8841 (tp) outliers start: 26 outliers final: 20 residues processed: 106 average time/residue: 0.1870 time to fit residues: 27.9508 Evaluate side-chains 113 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 653 ASP Chi-restraints excluded: chain H residue 273 LEU Chi-restraints excluded: chain H residue 427 SER Chi-restraints excluded: chain H residue 443 GLU Chi-restraints excluded: chain H residue 457 PHE Chi-restraints excluded: chain H residue 458 LEU Chi-restraints excluded: chain H residue 471 THR Chi-restraints excluded: chain H residue 499 GLU Chi-restraints excluded: chain H residue 514 SER Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 93 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 25 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 76 optimal weight: 0.4980 chunk 47 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 6 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 519 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.138996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.103205 restraints weight = 12200.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.105764 restraints weight = 8334.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.107480 restraints weight = 6495.144| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7820 Z= 0.239 Angle : 0.566 11.359 10542 Z= 0.302 Chirality : 0.039 0.177 1142 Planarity : 0.003 0.058 1342 Dihedral : 4.462 25.211 1021 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 3.00 % Allowed : 15.71 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.62 (0.29), residues: 915 helix: 1.96 (0.22), residues: 565 sheet: 1.59 (1.88), residues: 10 loop : -2.49 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 35 HIS 0.003 0.001 HIS C 345 PHE 0.024 0.001 PHE H 457 TYR 0.023 0.001 TYR H 529 ARG 0.002 0.000 ARG C 173 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 0.816 Fit side-chains revert: symmetry clash REVERT: C 90 LYS cc_start: 0.8604 (tppt) cc_final: 0.7902 (tttm) REVERT: C 143 HIS cc_start: 0.8051 (m-70) cc_final: 0.7581 (m90) REVERT: C 589 GLU cc_start: 0.6969 (mm-30) cc_final: 0.6685 (mm-30) REVERT: C 620 TYR cc_start: 0.7496 (m-80) cc_final: 0.6772 (m-80) REVERT: C 672 TYR cc_start: 0.8474 (t80) cc_final: 0.8198 (t80) REVERT: C 681 ARG cc_start: 0.7984 (ttm-80) cc_final: 0.7595 (ttm-80) REVERT: H 458 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7832 (mp) REVERT: H 473 MET cc_start: 0.7941 (tpp) cc_final: 0.7140 (tpp) REVERT: H 499 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7354 (tt0) outliers start: 25 outliers final: 23 residues processed: 100 average time/residue: 0.1760 time to fit residues: 24.8503 Evaluate side-chains 109 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 653 ASP Chi-restraints excluded: chain H residue 273 LEU Chi-restraints excluded: chain H residue 427 SER Chi-restraints excluded: chain H residue 443 GLU Chi-restraints excluded: chain H residue 457 PHE Chi-restraints excluded: chain H residue 458 LEU Chi-restraints excluded: chain H residue 471 THR Chi-restraints excluded: chain H residue 499 GLU Chi-restraints excluded: chain H residue 514 SER Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 93 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 7 optimal weight: 0.6980 chunk 20 optimal weight: 0.1980 chunk 52 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 12 optimal weight: 0.0270 chunk 84 optimal weight: 2.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 519 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.141560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.105855 restraints weight = 12235.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.108493 restraints weight = 8276.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.110138 restraints weight = 6418.260| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7820 Z= 0.175 Angle : 0.547 10.706 10542 Z= 0.290 Chirality : 0.037 0.187 1142 Planarity : 0.003 0.057 1342 Dihedral : 4.303 25.306 1021 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 3.36 % Allowed : 16.31 % Favored : 80.34 % 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: 0.68 (0.29), residues: 915 helix: 1.98 (0.22), residues: 573 sheet: 1.73 (1.87), residues: 10 loop : -2.55 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 167 HIS 0.004 0.001 HIS C 345 PHE 0.022 0.001 PHE H 457 TYR 0.022 0.001 TYR H 529 ARG 0.001 0.000 ARG H 511 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 0.831 Fit side-chains revert: symmetry clash REVERT: C 143 HIS cc_start: 0.8086 (m-70) cc_final: 0.7657 (m90) REVERT: C 589 GLU cc_start: 0.6998 (mm-30) cc_final: 0.6743 (mm-30) REVERT: C 620 TYR cc_start: 0.7497 (m-80) cc_final: 0.6735 (m-80) REVERT: C 672 TYR cc_start: 0.8457 (t80) cc_final: 0.8163 (t80) REVERT: C 681 ARG cc_start: 0.8027 (ttm-80) cc_final: 0.7626 (ttm-80) REVERT: H 458 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7743 (mp) REVERT: H 473 MET cc_start: 0.7920 (tpp) cc_final: 0.7068 (tpp) REVERT: H 499 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7333 (tt0) REVERT: R 50 MET cc_start: 0.8636 (mmm) cc_final: 0.8291 (mmm) outliers start: 28 outliers final: 24 residues processed: 108 average time/residue: 0.1853 time to fit residues: 28.2990 Evaluate side-chains 115 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 111 MET Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 653 ASP Chi-restraints excluded: chain H residue 273 LEU Chi-restraints excluded: chain H residue 427 SER Chi-restraints excluded: chain H residue 443 GLU Chi-restraints excluded: chain H residue 457 PHE Chi-restraints excluded: chain H residue 458 LEU Chi-restraints excluded: chain H residue 471 THR Chi-restraints excluded: chain H residue 499 GLU Chi-restraints excluded: chain H residue 514 SER Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain R residue 37 ILE Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 96 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 32 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 64 optimal weight: 0.0970 chunk 47 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 43 optimal weight: 0.2980 chunk 81 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 519 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.139914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.104552 restraints weight = 12405.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.107086 restraints weight = 8513.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.108824 restraints weight = 6637.546| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7820 Z= 0.196 Angle : 0.566 11.691 10542 Z= 0.300 Chirality : 0.038 0.198 1142 Planarity : 0.003 0.054 1342 Dihedral : 4.353 24.882 1021 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 3.24 % Allowed : 16.55 % Favored : 80.22 % 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: 0.76 (0.29), residues: 915 helix: 2.09 (0.22), residues: 566 sheet: 1.85 (1.96), residues: 10 loop : -2.48 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 167 HIS 0.004 0.001 HIS C 345 PHE 0.022 0.001 PHE H 457 TYR 0.022 0.001 TYR H 529 ARG 0.003 0.000 ARG C 173 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 88 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: C 143 HIS cc_start: 0.8068 (m-70) cc_final: 0.7640 (m90) REVERT: C 531 LEU cc_start: 0.6200 (OUTLIER) cc_final: 0.5935 (pt) REVERT: C 589 GLU cc_start: 0.7017 (mm-30) cc_final: 0.6720 (mm-30) REVERT: C 620 TYR cc_start: 0.7522 (m-80) cc_final: 0.6711 (m-80) REVERT: C 672 TYR cc_start: 0.8423 (t80) cc_final: 0.8100 (t80) REVERT: C 681 ARG cc_start: 0.8091 (ttm-80) cc_final: 0.7686 (ttm-80) REVERT: H 458 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7660 (mp) REVERT: H 473 MET cc_start: 0.7996 (tpp) cc_final: 0.7080 (tpp) REVERT: H 499 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7348 (tt0) REVERT: R 50 MET cc_start: 0.8625 (mmm) cc_final: 0.8257 (mmm) outliers start: 27 outliers final: 20 residues processed: 104 average time/residue: 0.2189 time to fit residues: 33.0741 Evaluate side-chains 110 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 653 ASP Chi-restraints excluded: chain H residue 273 LEU Chi-restraints excluded: chain H residue 427 SER Chi-restraints excluded: chain H residue 443 GLU Chi-restraints excluded: chain H residue 457 PHE Chi-restraints excluded: chain H residue 458 LEU Chi-restraints excluded: chain H residue 471 THR Chi-restraints excluded: chain H residue 499 GLU Chi-restraints excluded: chain H residue 514 SER Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain R residue 37 ILE Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 0 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 84 optimal weight: 0.2980 chunk 89 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 GLN C 254 GLN ** C 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 519 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.139485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.104021 restraints weight = 12394.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.106515 restraints weight = 8535.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.108204 restraints weight = 6674.324| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7820 Z= 0.214 Angle : 0.579 10.423 10542 Z= 0.308 Chirality : 0.039 0.232 1142 Planarity : 0.004 0.057 1342 Dihedral : 4.397 25.360 1021 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 2.88 % Allowed : 17.27 % Favored : 79.86 % 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: 0.78 (0.29), residues: 915 helix: 2.07 (0.22), residues: 565 sheet: 1.75 (1.97), residues: 10 loop : -2.39 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 35 HIS 0.003 0.001 HIS C 345 PHE 0.021 0.001 PHE H 457 TYR 0.022 0.001 TYR H 529 ARG 0.002 0.000 ARG C 173 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.861 Fit side-chains revert: symmetry clash REVERT: C 143 HIS cc_start: 0.8057 (m-70) cc_final: 0.7614 (m90) REVERT: C 322 MET cc_start: 0.8308 (ttm) cc_final: 0.8108 (ttm) REVERT: C 531 LEU cc_start: 0.6135 (OUTLIER) cc_final: 0.5849 (pt) REVERT: C 589 GLU cc_start: 0.7002 (mm-30) cc_final: 0.6710 (mm-30) REVERT: C 620 TYR cc_start: 0.7501 (m-80) cc_final: 0.6685 (m-80) REVERT: C 672 TYR cc_start: 0.8422 (t80) cc_final: 0.8093 (t80) REVERT: C 681 ARG cc_start: 0.8095 (ttm-80) cc_final: 0.7695 (ttm-80) REVERT: H 458 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7682 (mp) REVERT: H 473 MET cc_start: 0.7984 (tpp) cc_final: 0.7677 (tpp) REVERT: H 499 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7432 (tt0) outliers start: 24 outliers final: 19 residues processed: 101 average time/residue: 0.1758 time to fit residues: 25.2608 Evaluate side-chains 105 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 653 ASP Chi-restraints excluded: chain H residue 273 LEU Chi-restraints excluded: chain H residue 427 SER Chi-restraints excluded: chain H residue 443 GLU Chi-restraints excluded: chain H residue 457 PHE Chi-restraints excluded: chain H residue 458 LEU Chi-restraints excluded: chain H residue 471 THR Chi-restraints excluded: chain H residue 499 GLU Chi-restraints excluded: chain H residue 514 SER Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain R residue 88 LEU Chi-restraints excluded: chain R residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 24 optimal weight: 0.0670 chunk 15 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 50 optimal weight: 0.0050 chunk 82 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 49 optimal weight: 0.0020 chunk 30 optimal weight: 0.8980 chunk 77 optimal weight: 0.3980 overall best weight: 0.2140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 519 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.145458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.110480 restraints weight = 12398.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.113082 restraints weight = 8470.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.114829 restraints weight = 6582.084| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7820 Z= 0.146 Angle : 0.553 12.029 10542 Z= 0.290 Chirality : 0.037 0.229 1142 Planarity : 0.004 0.055 1342 Dihedral : 4.162 24.780 1021 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.64 % Allowed : 17.99 % Favored : 79.38 % 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: 0.96 (0.29), residues: 915 helix: 2.26 (0.22), residues: 566 sheet: 1.94 (1.90), residues: 10 loop : -2.43 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 452 HIS 0.005 0.001 HIS C 345 PHE 0.014 0.001 PHE H 457 TYR 0.018 0.001 TYR H 529 ARG 0.004 0.000 ARG C 173 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2742.27 seconds wall clock time: 49 minutes 2.59 seconds (2942.59 seconds total)