Starting phenix.real_space_refine on Mon Mar 11 08:01:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5s_12050/03_2024/7b5s_12050.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5s_12050/03_2024/7b5s_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5s_12050/03_2024/7b5s_12050.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5s_12050/03_2024/7b5s_12050.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5s_12050/03_2024/7b5s_12050.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5s_12050/03_2024/7b5s_12050.pdb" } 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 Residue "C TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 94": "OE1" <-> "OE2" Residue "C GLU 113": "OE1" <-> "OE2" Residue "C GLU 148": "OE1" <-> "OE2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "C GLU 215": "OE1" <-> "OE2" Residue "C GLU 241": "OE1" <-> "OE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C GLU 297": "OE1" <-> "OE2" Residue "C PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 420": "OE1" <-> "OE2" Residue "C GLU 438": "OE1" <-> "OE2" Residue "C GLU 439": "OE1" <-> "OE2" Residue "C GLU 443": "OE1" <-> "OE2" Residue "C GLU 560": "OE1" <-> "OE2" Residue "C GLU 589": "OE1" <-> "OE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "H GLU 102": "OE1" <-> "OE2" Residue "H ARG 271": "NH1" <-> "NH2" Residue "H GLU 492": "OE1" <-> "OE2" Residue "H ARG 530": "NH1" <-> "NH2" Residue "R GLU 23": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 4.59, per 1000 atoms: 0.60 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 - 3.50 Amino acid : False - 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: 2.86 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 0.76 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: 2.28 Time building geometry restraints manager: 3.11 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: 97.78 - 105.05: 67 105.05 - 112.32: 3889 112.32 - 119.59: 2697 119.59 - 126.86: 3799 126.86 - 134.14: 90 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 2.440 nonbonded pdb=" N GLU H 454 " pdb=" OE1 GLU H 454 " model vdw 2.191 2.520 nonbonded pdb=" OH TYR C 244 " pdb=" OE2 GLU C 271 " model vdw 2.200 2.440 nonbonded pdb=" OH TYR C 260 " pdb=" O LEU C 295 " model vdw 2.222 2.440 ... (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 ========== 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: 1.650 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: 6.970 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 25.920 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.740 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 0.852 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: 0.1856 time to fit residues: 27.2263 Evaluate side-chains 86 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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: 1.9990 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7820 Z= 0.263 Angle : 0.596 8.523 10542 Z= 0.321 Chirality : 0.039 0.200 1142 Planarity : 0.004 0.097 1342 Dihedral : 4.846 23.539 1023 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 1.56 % Allowed : 8.39 % Favored : 90.05 % 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: 0.02 (0.29), residues: 915 helix: 1.44 (0.22), residues: 562 sheet: 1.24 (1.83), residues: 10 loop : -2.61 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 452 HIS 0.004 0.001 HIS C 345 PHE 0.030 0.002 PHE H 457 TYR 0.026 0.002 TYR H 529 ARG 0.004 0.000 ARG C 173 *********************** 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 111 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: C 143 HIS cc_start: 0.8105 (m-70) cc_final: 0.7740 (m90) REVERT: H 275 TRP cc_start: 0.7197 (m100) cc_final: 0.6987 (m100) REVERT: H 497 ASP cc_start: 0.7539 (t0) cc_final: 0.7296 (t0) REVERT: R 54 ILE cc_start: 0.9131 (tp) cc_final: 0.8793 (tp) outliers start: 13 outliers final: 13 residues processed: 106 average time/residue: 0.1844 time to fit residues: 27.6535 Evaluate side-chains 102 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 C residue 585 LEU Chi-restraints excluded: chain C residue 634 ASP Chi-restraints excluded: chain H residue 273 LEU Chi-restraints excluded: chain H residue 471 THR Chi-restraints excluded: chain H residue 488 SER Chi-restraints excluded: chain H residue 499 GLU Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 40 ASP 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 46 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 83 optimal weight: 0.5980 chunk 90 optimal weight: 0.7980 chunk 74 optimal weight: 0.1980 chunk 82 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 67 optimal weight: 5.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 304 HIS ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1386 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= 0.185 Angle : 0.539 6.857 10542 Z= 0.289 Chirality : 0.037 0.156 1142 Planarity : 0.004 0.074 1342 Dihedral : 4.589 24.025 1021 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 1.80 % Allowed : 12.35 % Favored : 85.85 % 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: 0.38 (0.29), residues: 915 helix: 1.77 (0.22), residues: 567 sheet: 1.43 (1.84), residues: 10 loop : -2.62 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 452 HIS 0.004 0.001 HIS C 345 PHE 0.023 0.001 PHE H 457 TYR 0.022 0.001 TYR H 529 ARG 0.003 0.000 ARG C 41 *********************** 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 114 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: C 90 LYS cc_start: 0.8684 (tppt) cc_final: 0.7987 (tttm) REVERT: C 143 HIS cc_start: 0.8012 (m-70) cc_final: 0.7669 (m90) REVERT: C 427 ASP cc_start: 0.8140 (t0) cc_final: 0.7896 (t0) REVERT: C 488 MET cc_start: 0.8680 (tpt) cc_final: 0.8269 (tpt) REVERT: C 589 GLU cc_start: 0.7170 (mm-30) cc_final: 0.6909 (mm-30) REVERT: H 450 MET cc_start: 0.4282 (mmm) cc_final: 0.4051 (mmt) REVERT: H 473 MET cc_start: 0.7961 (tpp) cc_final: 0.7328 (tpp) REVERT: H 497 ASP cc_start: 0.7730 (t0) cc_final: 0.7435 (t0) REVERT: R 54 ILE cc_start: 0.9148 (tp) cc_final: 0.8846 (tp) outliers start: 15 outliers final: 8 residues processed: 104 average time/residue: 0.1896 time to fit residues: 28.0302 Evaluate side-chains 97 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 89 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 382 MET 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 471 THR 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 82 optimal weight: 0.9990 chunk 62 optimal weight: 8.9990 chunk 43 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 83 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 74 optimal weight: 0.0870 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7820 Z= 0.207 Angle : 0.540 9.270 10542 Z= 0.290 Chirality : 0.037 0.131 1142 Planarity : 0.004 0.065 1342 Dihedral : 4.522 25.676 1021 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 2.52 % Allowed : 13.91 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.29), residues: 915 helix: 1.89 (0.22), residues: 567 sheet: 1.33 (1.85), residues: 10 loop : -2.58 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 452 HIS 0.003 0.001 HIS C 345 PHE 0.022 0.001 PHE H 457 TYR 0.023 0.001 TYR H 529 ARG 0.003 0.000 ARG C 41 *********************** 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 112 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 91 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: C 90 LYS cc_start: 0.8646 (tppt) cc_final: 0.7994 (tttm) REVERT: C 143 HIS cc_start: 0.8044 (m-70) cc_final: 0.7647 (m90) REVERT: C 589 GLU cc_start: 0.7083 (mm-30) cc_final: 0.6768 (mm-30) REVERT: H 449 ASN cc_start: 0.6592 (t0) cc_final: 0.6243 (t0) REVERT: H 450 MET cc_start: 0.4752 (mmm) cc_final: 0.4547 (mmt) REVERT: H 458 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8060 (mp) REVERT: H 473 MET cc_start: 0.7925 (tpp) cc_final: 0.7213 (tpp) REVERT: H 497 ASP cc_start: 0.7865 (t0) cc_final: 0.7570 (t0) REVERT: R 50 MET cc_start: 0.8644 (mmm) cc_final: 0.8370 (mmm) REVERT: R 54 ILE cc_start: 0.9179 (tp) cc_final: 0.8948 (tp) outliers start: 21 outliers final: 14 residues processed: 102 average time/residue: 0.1883 time to fit residues: 26.9535 Evaluate side-chains 105 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 90 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 352 ILE Chi-restraints excluded: chain C residue 382 MET 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 443 GLU 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 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 50 optimal weight: 0.2980 chunk 1 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 29 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 254 GLN ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7820 Z= 0.193 Angle : 0.519 7.287 10542 Z= 0.281 Chirality : 0.037 0.177 1142 Planarity : 0.003 0.058 1342 Dihedral : 4.414 26.781 1021 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 2.40 % Allowed : 15.59 % Favored : 82.01 % 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: 0.65 (0.29), residues: 915 helix: 2.01 (0.22), residues: 567 sheet: 1.29 (1.88), residues: 10 loop : -2.57 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 452 HIS 0.004 0.001 HIS C 345 PHE 0.023 0.001 PHE H 457 TYR 0.022 0.001 TYR H 529 ARG 0.002 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 113 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 93 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: C 90 LYS cc_start: 0.8620 (tppt) cc_final: 0.8313 (mmtm) REVERT: C 143 HIS cc_start: 0.8076 (m-70) cc_final: 0.7707 (m90) REVERT: C 589 GLU cc_start: 0.7089 (mm-30) cc_final: 0.6777 (mm-30) REVERT: H 458 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8063 (mp) REVERT: H 473 MET cc_start: 0.7941 (tpp) cc_final: 0.7230 (tpp) REVERT: H 497 ASP cc_start: 0.7821 (t0) cc_final: 0.7518 (t0) REVERT: H 499 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7263 (tt0) REVERT: R 50 MET cc_start: 0.8645 (mmm) cc_final: 0.8346 (mmm) REVERT: R 54 ILE cc_start: 0.9160 (tp) cc_final: 0.8940 (tp) outliers start: 20 outliers final: 16 residues processed: 103 average time/residue: 0.1865 time to fit residues: 27.0292 Evaluate side-chains 105 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 87 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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 349 LEU Chi-restraints excluded: chain C residue 352 ILE Chi-restraints excluded: chain C residue 382 MET 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 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 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 80 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 73 optimal weight: 0.1980 chunk 41 optimal weight: 0.2980 chunk 7 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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** ** H 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 519 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7820 Z= 0.174 Angle : 0.530 14.129 10542 Z= 0.281 Chirality : 0.036 0.146 1142 Planarity : 0.003 0.054 1342 Dihedral : 4.324 26.745 1021 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 3.12 % Allowed : 15.83 % Favored : 81.06 % 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: 0.72 (0.29), residues: 915 helix: 2.04 (0.22), residues: 573 sheet: 1.33 (1.88), residues: 10 loop : -2.56 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 452 HIS 0.004 0.001 HIS C 345 PHE 0.024 0.001 PHE H 457 TYR 0.022 0.001 TYR H 529 ARG 0.002 0.000 ARG C 173 *********************** 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 119 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 93 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: C 90 LYS cc_start: 0.8526 (tppt) cc_final: 0.8306 (mmtm) REVERT: C 143 HIS cc_start: 0.7998 (m-70) cc_final: 0.7696 (m90) REVERT: C 558 GLU cc_start: 0.7966 (tp30) cc_final: 0.7714 (tp30) REVERT: C 589 GLU cc_start: 0.6989 (mm-30) cc_final: 0.6694 (mm-30) REVERT: H 458 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7952 (mp) REVERT: H 473 MET cc_start: 0.7925 (tpp) cc_final: 0.7158 (tpp) REVERT: H 497 ASP cc_start: 0.7833 (t0) cc_final: 0.7506 (t0) REVERT: H 499 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7224 (tt0) REVERT: R 50 MET cc_start: 0.8651 (mmm) cc_final: 0.8325 (mmm) REVERT: R 54 ILE cc_start: 0.9144 (tp) cc_final: 0.8927 (tp) outliers start: 26 outliers final: 19 residues processed: 109 average time/residue: 0.1887 time to fit residues: 28.6108 Evaluate side-chains 111 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 90 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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 172 PHE Chi-restraints excluded: chain C residue 318 ASP 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 445 THR 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 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 10 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 54 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 519 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7820 Z= 0.236 Angle : 0.551 12.851 10542 Z= 0.294 Chirality : 0.038 0.146 1142 Planarity : 0.003 0.053 1342 Dihedral : 4.460 28.657 1021 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 3.48 % Allowed : 16.31 % 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: 0.69 (0.29), residues: 915 helix: 2.04 (0.22), residues: 565 sheet: 1.20 (1.90), residues: 10 loop : -2.50 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 35 HIS 0.003 0.001 HIS C 343 PHE 0.024 0.001 PHE H 457 TYR 0.023 0.001 TYR H 529 ARG 0.004 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 119 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 90 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: C 90 LYS cc_start: 0.8616 (tppt) cc_final: 0.7922 (tttm) REVERT: C 143 HIS cc_start: 0.7934 (m-70) cc_final: 0.7584 (m90) REVERT: C 589 GLU cc_start: 0.7070 (mm-30) cc_final: 0.6727 (mm-30) REVERT: C 672 TYR cc_start: 0.8492 (t80) cc_final: 0.8248 (t80) REVERT: H 458 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.7971 (mp) REVERT: H 473 MET cc_start: 0.7894 (tpp) cc_final: 0.7142 (tpp) REVERT: H 497 ASP cc_start: 0.7837 (t0) cc_final: 0.7498 (t0) REVERT: H 499 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7267 (tt0) REVERT: R 54 ILE cc_start: 0.9157 (tp) cc_final: 0.8952 (tp) outliers start: 29 outliers final: 22 residues processed: 111 average time/residue: 0.1849 time to fit residues: 28.7711 Evaluate side-chains 112 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 88 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 172 PHE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 318 ASP 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 445 THR 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 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 40 ASP 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 26 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 77 optimal weight: 0.0980 chunk 82 optimal weight: 0.5980 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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** ** H 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 519 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7820 Z= 0.202 Angle : 0.549 14.421 10542 Z= 0.288 Chirality : 0.037 0.166 1142 Planarity : 0.003 0.051 1342 Dihedral : 4.409 28.673 1021 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 3.24 % Allowed : 17.39 % 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: 0.77 (0.29), residues: 915 helix: 2.08 (0.22), residues: 567 sheet: 1.28 (1.96), residues: 10 loop : -2.45 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 35 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 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 118 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 91 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: C 90 LYS cc_start: 0.8579 (tppt) cc_final: 0.7910 (tttm) REVERT: C 143 HIS cc_start: 0.7935 (m-70) cc_final: 0.7573 (m90) REVERT: C 531 LEU cc_start: 0.6243 (OUTLIER) cc_final: 0.5962 (pt) REVERT: C 589 GLU cc_start: 0.6981 (mm-30) cc_final: 0.6610 (mm-30) REVERT: C 672 TYR cc_start: 0.8511 (t80) cc_final: 0.8267 (t80) REVERT: H 458 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.7949 (mp) REVERT: H 473 MET cc_start: 0.7901 (tpp) cc_final: 0.7662 (tpp) REVERT: H 497 ASP cc_start: 0.7868 (t0) cc_final: 0.7531 (t0) REVERT: H 499 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7267 (tt0) REVERT: R 50 MET cc_start: 0.8683 (mmm) cc_final: 0.8352 (mmm) REVERT: R 54 ILE cc_start: 0.9144 (tp) cc_final: 0.8936 (tp) outliers start: 27 outliers final: 21 residues processed: 109 average time/residue: 0.1931 time to fit residues: 29.7652 Evaluate side-chains 112 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 88 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 111 MET Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 318 ASP 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 445 THR 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 2.9990 chunk 49 optimal weight: 0.2980 chunk 35 optimal weight: 0.0270 chunk 64 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 82 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 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 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 519 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2183 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= 0.171 Angle : 0.538 14.083 10542 Z= 0.281 Chirality : 0.037 0.152 1142 Planarity : 0.003 0.050 1342 Dihedral : 4.277 28.469 1021 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 2.76 % Allowed : 17.99 % Favored : 79.26 % 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: 0.89 (0.29), residues: 915 helix: 2.18 (0.22), residues: 567 sheet: 1.33 (1.99), residues: 10 loop : -2.41 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 452 HIS 0.004 0.001 HIS C 345 PHE 0.021 0.001 PHE H 457 TYR 0.021 0.001 TYR H 529 ARG 0.002 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 118 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 95 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: C 90 LYS cc_start: 0.8553 (tppt) cc_final: 0.7867 (tttm) REVERT: C 143 HIS cc_start: 0.7882 (m-70) cc_final: 0.7557 (m90) REVERT: C 531 LEU cc_start: 0.6193 (OUTLIER) cc_final: 0.5908 (pt) REVERT: C 589 GLU cc_start: 0.6862 (mm-30) cc_final: 0.6543 (mm-30) REVERT: C 672 TYR cc_start: 0.8498 (t80) cc_final: 0.8257 (t80) REVERT: H 458 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7970 (mp) REVERT: H 473 MET cc_start: 0.7926 (tpp) cc_final: 0.7113 (tpp) REVERT: H 497 ASP cc_start: 0.7863 (t0) cc_final: 0.7538 (t0) REVERT: H 499 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7281 (tt0) REVERT: R 50 MET cc_start: 0.8666 (mmm) cc_final: 0.8339 (mmm) REVERT: R 54 ILE cc_start: 0.9111 (tp) cc_final: 0.8909 (tp) outliers start: 23 outliers final: 19 residues processed: 108 average time/residue: 0.1946 time to fit residues: 29.0107 Evaluate side-chains 112 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 90 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 111 MET Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 318 ASP 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 445 THR 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 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 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 41 optimal weight: 0.6980 chunk 60 optimal weight: 0.0270 chunk 91 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 72 optimal weight: 0.4980 chunk 7 optimal weight: 0.0670 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 77 optimal weight: 0.3980 chunk 22 optimal weight: 0.9990 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 404 ASN ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 519 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 7820 Z= 0.149 Angle : 0.529 14.010 10542 Z= 0.273 Chirality : 0.036 0.173 1142 Planarity : 0.003 0.050 1342 Dihedral : 4.148 28.256 1021 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 2.76 % Allowed : 18.82 % Favored : 78.42 % 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: 1.00 (0.29), residues: 915 helix: 2.27 (0.22), residues: 567 sheet: 1.42 (1.95), residues: 10 loop : -2.36 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 452 HIS 0.004 0.001 HIS C 345 PHE 0.018 0.001 PHE H 457 TYR 0.020 0.001 TYR H 529 ARG 0.003 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 116 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 93 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: C 143 HIS cc_start: 0.7843 (m-70) cc_final: 0.7510 (m90) REVERT: C 458 ASP cc_start: 0.7512 (p0) cc_final: 0.7305 (p0) REVERT: C 531 LEU cc_start: 0.6093 (OUTLIER) cc_final: 0.5816 (pt) REVERT: C 589 GLU cc_start: 0.6805 (mm-30) cc_final: 0.6500 (mm-30) REVERT: C 672 TYR cc_start: 0.8485 (t80) cc_final: 0.8253 (t80) REVERT: H 458 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7918 (mp) REVERT: H 473 MET cc_start: 0.7927 (tpp) cc_final: 0.7129 (tpp) REVERT: H 497 ASP cc_start: 0.7830 (t0) cc_final: 0.7494 (t0) REVERT: H 499 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7268 (tt0) REVERT: R 54 ILE cc_start: 0.9120 (tp) cc_final: 0.8896 (tp) outliers start: 23 outliers final: 14 residues processed: 107 average time/residue: 0.1871 time to fit residues: 28.0589 Evaluate side-chains 108 residues out of total 846 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 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 531 LEU Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 585 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 458 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 73 optimal weight: 0.6980 chunk 30 optimal weight: 0.2980 chunk 75 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 64 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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** ** H 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 519 GLN R 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.142512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.106668 restraints weight = 12237.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.109249 restraints weight = 8328.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.111050 restraints weight = 6492.123| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7820 Z= 0.182 Angle : 0.548 16.497 10542 Z= 0.282 Chirality : 0.037 0.250 1142 Planarity : 0.003 0.050 1342 Dihedral : 4.214 28.255 1021 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 2.28 % Allowed : 19.42 % Favored : 78.30 % 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: 0.89 (0.29), residues: 915 helix: 2.12 (0.22), residues: 573 sheet: 1.35 (1.97), residues: 10 loop : -2.37 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 35 HIS 0.004 0.001 HIS C 345 PHE 0.019 0.001 PHE H 457 TYR 0.022 0.001 TYR H 529 ARG 0.002 0.000 ARG H 511 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1687.29 seconds wall clock time: 31 minutes 27.83 seconds (1887.83 seconds total)