Starting phenix.real_space_refine on Thu Mar 13 12:33:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oni_12995/03_2025/7oni_12995.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oni_12995/03_2025/7oni_12995.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7oni_12995/03_2025/7oni_12995.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oni_12995/03_2025/7oni_12995.map" model { file = "/net/cci-nas-00/data/ceres_data/7oni_12995/03_2025/7oni_12995.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oni_12995/03_2025/7oni_12995.cif" } resolution = 3.4 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= 0.001 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 7 6.06 5 S 66 5.16 5 C 5612 2.51 5 N 1547 2.21 5 O 1608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 8840 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 4604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4604 Classifications: {'peptide': 599} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 16, 'TRANS': 582} Chain breaks: 4 Unresolved non-hydrogen bonds: 317 Unresolved non-hydrogen angles: 377 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 23, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 197 Chain: "H" Number of atoms: 2965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 2965 Classifications: {'peptide': 380} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 15, 'TRANS': 364} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 235 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 3, 'PHE:plan': 3, 'GLU:plan': 9, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 146 Chain: "R" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 665 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "N" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 599 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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 6210 SG CYS H 257 49.362 39.391 59.631 1.00 87.84 S ATOM 6236 SG CYS H 260 46.583 36.946 60.532 1.00 90.61 S ATOM 6319 SG CYS H 270 49.718 35.412 59.286 1.00 79.10 S ATOM 5323 SG CYS H 139 13.132 27.136 34.761 1.00299.90 S ATOM 5339 SG CYS H 142 9.622 27.375 35.933 1.00303.51 S ATOM 5456 SG CYS H 161 11.245 30.310 34.671 1.00269.35 S ATOM 5473 SG CYS H 164 12.210 29.163 38.092 1.00253.44 S ATOM 5985 SG CYS H 228 40.696 49.936 58.529 1.00117.41 S ATOM 6015 SG CYS H 233 38.820 52.969 58.117 1.00130.21 S ATOM 6144 SG CYS H 249 42.510 53.091 57.789 1.00120.06 S ATOM 6169 SG CYS H 252 40.705 52.527 61.323 1.00121.79 S ATOM 5425 SG CYS H 156 25.478 26.153 32.288 1.00241.79 S ATOM 5607 SG CYS H 183 23.516 26.317 35.438 1.00234.27 S ATOM 5636 SG CYS H 188 27.005 24.346 35.272 1.00228.45 S ATOM 7751 SG CYS R 50 78.829 36.177 71.964 1.00 60.28 S ATOM 7770 SG CYS R 53 76.587 39.458 72.451 1.00 61.23 S ATOM 8028 SG CYS R 88 78.219 37.809 75.354 1.00 69.80 S ATOM 7831 SG CYS R 61 79.977 42.376 77.253 1.00 73.46 S ATOM 7856 SG CYS R 64 82.743 43.899 79.259 1.00 74.94 S ATOM 7909 SG CYS R 73 83.434 41.796 76.051 1.00 78.73 S ATOM 8022 SG CYS R 87 82.459 40.084 79.076 1.00 73.60 S ATOM 7963 SG CYS R 80 82.549 24.049 70.089 1.00 83.55 S ATOM 8118 SG CYS R 99 79.153 25.803 70.901 1.00 73.85 S ATOM 8139 SG CYS R 102 79.582 22.556 68.730 1.00 80.17 S Time building chain proxies: 6.45, per 1000 atoms: 0.73 Number of scatterers: 8840 At special positions: 0 Unit cell: (136.192, 117.466, 125.126, 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 7 29.99 S 66 16.00 O 1608 8.00 N 1547 7.00 C 5612 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.22 Conformation dependent library (CDL) restraints added in 999.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H 501 " pdb="ZN ZN H 501 " - pdb=" NE2 HIS H 265 " pdb="ZN ZN H 501 " - pdb=" SG CYS H 260 " pdb="ZN ZN H 501 " - pdb=" SG CYS H 270 " pdb="ZN ZN H 501 " - pdb=" SG CYS H 257 " pdb=" ZN H 502 " pdb="ZN ZN H 502 " - pdb=" SG CYS H 161 " pdb="ZN ZN H 502 " - pdb=" SG CYS H 139 " pdb="ZN ZN H 502 " - pdb=" SG CYS H 164 " pdb="ZN ZN H 502 " - pdb=" SG CYS H 142 " pdb=" ZN H 503 " pdb="ZN ZN H 503 " - pdb=" SG CYS H 252 " pdb="ZN ZN H 503 " - pdb=" SG CYS H 228 " pdb="ZN ZN H 503 " - pdb=" SG CYS H 249 " pdb="ZN ZN H 503 " - pdb=" SG CYS H 233 " pdb=" ZN H 504 " pdb="ZN ZN H 504 " - pdb=" ND1 HIS H 158 " pdb="ZN ZN H 504 " - pdb=" SG CYS H 156 " pdb="ZN ZN H 504 " - pdb=" SG CYS H 188 " pdb="ZN ZN H 504 " - pdb=" SG CYS H 183 " pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 85 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 50 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 53 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 88 " pdb=" ZN R 202 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 61 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 64 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 73 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 87 " pdb=" ZN R 203 " pdb="ZN ZN R 203 " - pdb=" ND1 HIS R 82 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 80 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 99 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 102 " Number of angles added : 30 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2214 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 9 sheets defined 60.4% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'C' and resid 152 through 169 removed outlier: 3.638A pdb=" N GLN C 156 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET C 160 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS C 161 " --> pdb=" O ASP C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 188 removed outlier: 3.709A pdb=" N VAL C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N CYS C 188 " --> pdb=" O TYR C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 201 Processing helix chain 'C' and resid 202 through 249 Proline residue: C 219 - end of helix removed outlier: 7.935A pdb=" N VAL C 227 " --> pdb=" O GLN C 223 " (cutoff:3.500A) removed outlier: 9.246A pdb=" N GLN C 228 " --> pdb=" O GLN C 224 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASN C 229 " --> pdb=" O ASN C 225 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS C 232 " --> pdb=" O GLN C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 270 Processing helix chain 'C' and resid 273 through 285 removed outlier: 3.701A pdb=" N ILE C 277 " --> pdb=" O PHE C 273 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU C 280 " --> pdb=" O THR C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 303 removed outlier: 4.033A pdb=" N LEU C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LYS C 302 " --> pdb=" O SER C 298 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 329 Processing helix chain 'C' and resid 336 through 360 removed outlier: 3.669A pdb=" N TYR C 340 " --> pdb=" O ASP C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 378 removed outlier: 3.506A pdb=" N ALA C 375 " --> pdb=" O LYS C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 417 Processing helix chain 'C' and resid 419 through 425 removed outlier: 3.920A pdb=" N LYS C 424 " --> pdb=" O PRO C 420 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU C 425 " --> pdb=" O LEU C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 442 Processing helix chain 'C' and resid 446 through 465 removed outlier: 4.013A pdb=" N PHE C 450 " --> pdb=" O ASN C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 484 Processing helix chain 'C' and resid 486 through 515 removed outlier: 3.800A pdb=" N VAL C 490 " --> pdb=" O PRO C 486 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN C 491 " --> pdb=" O ALA C 487 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN C 508 " --> pdb=" O GLU C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 524 No H-bonds generated for 'chain 'C' and resid 522 through 524' Processing helix chain 'C' and resid 548 through 553 Processing helix chain 'C' and resid 554 through 566 removed outlier: 4.222A pdb=" N ASN C 565 " --> pdb=" O PHE C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 605 removed outlier: 3.682A pdb=" N ALA C 605 " --> pdb=" O ALA C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 623 removed outlier: 3.557A pdb=" N LYS C 620 " --> pdb=" O PHE C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 639 Processing helix chain 'C' and resid 656 through 660 Processing helix chain 'C' and resid 700 through 726 removed outlier: 3.779A pdb=" N ASN C 704 " --> pdb=" O ARG C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 731 through 742 removed outlier: 3.815A pdb=" N GLN C 735 " --> pdb=" O ASN C 731 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR C 736 " --> pdb=" O ALA C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 762 Processing helix chain 'H' and resid 41 through 46 removed outlier: 3.901A pdb=" N ASP H 45 " --> pdb=" O GLY H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 85 removed outlier: 3.756A pdb=" N GLU H 70 " --> pdb=" O TYR H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 98 Processing helix chain 'H' and resid 101 through 112 Processing helix chain 'H' and resid 112 through 120 removed outlier: 3.625A pdb=" N LEU H 116 " --> pdb=" O ASN H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 175 Processing helix chain 'H' and resid 193 through 198 Processing helix chain 'H' and resid 199 through 201 No H-bonds generated for 'chain 'H' and resid 199 through 201' Processing helix chain 'H' and resid 203 through 222 Processing helix chain 'H' and resid 271 through 282 removed outlier: 3.766A pdb=" N ASP H 282 " --> pdb=" O THR H 278 " (cutoff:3.500A) Processing helix chain 'H' and resid 353 through 381 removed outlier: 3.552A pdb=" N TYR H 368 " --> pdb=" O LYS H 364 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ARG H 371 " --> pdb=" O PHE H 367 " (cutoff:3.500A) Processing helix chain 'H' and resid 381 through 399 removed outlier: 4.010A pdb=" N THR H 385 " --> pdb=" O ALA H 381 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG H 396 " --> pdb=" O LYS H 392 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASN H 399 " --> pdb=" O GLU H 395 " (cutoff:3.500A) Processing helix chain 'H' and resid 408 through 426 removed outlier: 3.994A pdb=" N ASN H 412 " --> pdb=" O GLN H 408 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR H 426 " --> pdb=" O TYR H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 427 through 433 Processing helix chain 'H' and resid 437 through 462 removed outlier: 3.900A pdb=" N LYS H 441 " --> pdb=" O GLY H 437 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU H 442 " --> pdb=" O PRO H 438 " (cutoff:3.500A) Processing helix chain 'H' and resid 468 through 489 removed outlier: 4.175A pdb=" N ASP H 489 " --> pdb=" O THR H 485 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 68 Processing helix chain 'R' and resid 86 through 96 Processing helix chain 'N' and resid 22 through 34 Processing helix chain 'N' and resid 37 through 39 No H-bonds generated for 'chain 'N' and resid 37 through 39' Processing helix chain 'N' and resid 55 through 60 Processing sheet with id=AA1, first strand: chain 'C' and resid 526 through 527 removed outlier: 5.664A pdb=" N LEU R 32 " --> pdb=" O THR C 583 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N THR C 583 " --> pdb=" O LEU R 32 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN C 579 " --> pdb=" O ASN R 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 530 through 532 removed outlier: 3.535A pdb=" N SER R 42 " --> pdb=" O LYS C 570 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 614 through 615 Processing sheet with id=AA4, first strand: chain 'C' and resid 728 through 729 removed outlier: 3.860A pdb=" N ILE C 729 " --> pdb=" O PHE C 776 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE C 776 " --> pdb=" O ILE C 729 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 62 through 64 Processing sheet with id=AA6, first strand: chain 'H' and resid 151 through 152 Processing sheet with id=AA7, first strand: chain 'H' and resid 246 through 249 removed outlier: 3.734A pdb=" N GLU H 254 " --> pdb=" O CYS H 249 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 84 through 85 removed outlier: 4.499A pdb=" N ARG R 110 " --> pdb=" O TRP R 77 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 12 through 16 509 hydrogen bonds defined for protein. 1494 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: 2.46 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2920 1.35 - 1.46: 2015 1.46 - 1.58: 3965 1.58 - 1.70: 0 1.70 - 1.82: 97 Bond restraints: 8997 Sorted by residual: bond pdb=" N ASN C 201 " pdb=" CA ASN C 201 " ideal model delta sigma weight residual 1.453 1.489 -0.037 1.31e-02 5.83e+03 7.81e+00 bond pdb=" N PHE C 202 " pdb=" CA PHE C 202 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.78e+00 bond pdb=" N GLU C 203 " pdb=" CA GLU C 203 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.42e+00 bond pdb=" N ASP C 200 " pdb=" CA ASP C 200 " ideal model delta sigma weight residual 1.463 1.490 -0.027 1.08e-02 8.57e+03 6.25e+00 bond pdb=" N LYS C 204 " pdb=" CA LYS C 204 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.19e-02 7.06e+03 5.86e+00 ... (remaining 8992 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 12005 1.81 - 3.62: 154 3.62 - 5.42: 26 5.42 - 7.23: 5 7.23 - 9.04: 1 Bond angle restraints: 12191 Sorted by residual: angle pdb=" CA ASN C 201 " pdb=" C ASN C 201 " pdb=" O ASN C 201 " ideal model delta sigma weight residual 121.94 116.40 5.54 1.15e+00 7.56e-01 2.32e+01 angle pdb=" N LYS C 743 " pdb=" CA LYS C 743 " pdb=" C LYS C 743 " ideal model delta sigma weight residual 114.04 110.03 4.01 1.24e+00 6.50e-01 1.04e+01 angle pdb=" CB MET C 513 " pdb=" CG MET C 513 " pdb=" SD MET C 513 " ideal model delta sigma weight residual 112.70 121.74 -9.04 3.00e+00 1.11e-01 9.08e+00 angle pdb=" N THR C 251 " pdb=" CA THR C 251 " pdb=" C THR C 251 " ideal model delta sigma weight residual 114.56 110.81 3.75 1.27e+00 6.20e-01 8.70e+00 angle pdb=" CA LYS C 204 " pdb=" C LYS C 204 " pdb=" O LYS C 204 " ideal model delta sigma weight residual 120.82 117.76 3.06 1.05e+00 9.07e-01 8.51e+00 ... (remaining 12186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.45: 4852 16.45 - 32.90: 468 32.90 - 49.35: 115 49.35 - 65.80: 15 65.80 - 82.25: 9 Dihedral angle restraints: 5459 sinusoidal: 2072 harmonic: 3387 Sorted by residual: dihedral pdb=" CA ASN C 607 " pdb=" C ASN C 607 " pdb=" N GLN C 608 " pdb=" CA GLN C 608 " ideal model delta harmonic sigma weight residual 180.00 161.09 18.91 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA GLY C 283 " pdb=" C GLY C 283 " pdb=" N MET C 284 " pdb=" CA MET C 284 " ideal model delta harmonic sigma weight residual -180.00 -161.16 -18.84 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA ILE C 773 " pdb=" C ILE C 773 " pdb=" N ASN C 774 " pdb=" CA ASN C 774 " ideal model delta harmonic sigma weight residual 180.00 162.61 17.39 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 5456 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 961 0.034 - 0.067: 314 0.067 - 0.101: 80 0.101 - 0.134: 32 0.134 - 0.168: 3 Chirality restraints: 1390 Sorted by residual: chirality pdb=" CA GLU C 203 " pdb=" N GLU C 203 " pdb=" C GLU C 203 " pdb=" CB GLU C 203 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.02e-01 chirality pdb=" CA GLU N 28 " pdb=" N GLU N 28 " pdb=" C GLU N 28 " pdb=" CB GLU N 28 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.76e-01 chirality pdb=" CA GLU C 308 " pdb=" N GLU C 308 " pdb=" C GLU C 308 " pdb=" CB GLU C 308 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.58e-01 ... (remaining 1387 not shown) Planarity restraints: 1559 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 419 " 0.029 5.00e-02 4.00e+02 4.40e-02 3.09e+00 pdb=" N PRO C 420 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO C 420 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 420 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 184 " -0.003 2.00e-02 2.50e+03 9.22e-03 1.70e+00 pdb=" CG TYR C 184 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR C 184 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR C 184 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR C 184 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR C 184 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR C 184 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 184 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 199 " 0.006 2.00e-02 2.50e+03 1.13e-02 1.27e+00 pdb=" C ARG C 199 " -0.020 2.00e-02 2.50e+03 pdb=" O ARG C 199 " 0.007 2.00e-02 2.50e+03 pdb=" N ASP C 200 " 0.007 2.00e-02 2.50e+03 ... (remaining 1556 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1280 2.76 - 3.29: 8571 3.29 - 3.83: 14303 3.83 - 4.36: 15753 4.36 - 4.90: 28030 Nonbonded interactions: 67937 Sorted by model distance: nonbonded pdb=" O ASN C 267 " pdb=" OG1 THR C 271 " model vdw 2.219 3.040 nonbonded pdb=" OE1 GLU C 755 " pdb=" NE2 GLN C 756 " model vdw 2.302 3.120 nonbonded pdb=" OD1 ASN N 51 " pdb=" OH TYR N 59 " model vdw 2.312 3.040 nonbonded pdb=" OE1 GLU H 57 " pdb=" OH TYR H 264 " model vdw 2.327 3.040 nonbonded pdb=" OE1 GLU C 594 " pdb=" ND2 ASN C 687 " model vdw 2.330 3.120 ... (remaining 67932 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.410 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.990 Find NCS groups from input model: 0.080 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 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 : 0.003 0.037 8997 Z= 0.172 Angle : 0.535 9.039 12191 Z= 0.294 Chirality : 0.038 0.168 1390 Planarity : 0.003 0.044 1559 Dihedral : 14.036 82.254 3245 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.82 (0.26), residues: 1119 helix: 1.86 (0.21), residues: 639 sheet: -0.68 (0.62), residues: 70 loop : -1.41 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 41 HIS 0.002 0.000 HIS R 85 PHE 0.008 0.001 PHE H 256 TYR 0.018 0.001 TYR C 184 ARG 0.003 0.000 ARG H 482 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.2260 time to fit residues: 30.8714 Evaluate side-chains 67 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.0270 chunk 84 optimal weight: 0.8980 chunk 47 optimal weight: 0.0670 chunk 28 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 101 optimal weight: 0.0970 overall best weight: 0.2974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 115 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 = 0.3546 r_free = 0.3546 target = 0.074196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.052701 restraints weight = 29170.860| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.90 r_work: 0.2877 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2880 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2878 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 8997 Z= 0.153 Angle : 0.498 6.862 12191 Z= 0.263 Chirality : 0.038 0.146 1390 Planarity : 0.003 0.043 1559 Dihedral : 3.734 17.499 1228 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.56 % Allowed : 7.15 % Favored : 92.29 % 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: 1.03 (0.26), residues: 1119 helix: 1.98 (0.21), residues: 646 sheet: -0.69 (0.67), residues: 64 loop : -1.26 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 573 HIS 0.004 0.001 HIS H 477 PHE 0.020 0.001 PHE C 202 TYR 0.011 0.001 TYR H 38 ARG 0.003 0.000 ARG C 167 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 1.324 Fit side-chains revert: symmetry clash REVERT: N 52 ASP cc_start: 0.7628 (t0) cc_final: 0.7328 (t0) outliers start: 5 outliers final: 2 residues processed: 81 average time/residue: 0.2071 time to fit residues: 25.6791 Evaluate side-chains 69 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 655 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 45 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 73 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 115 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 = 0.3512 r_free = 0.3512 target = 0.072640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.050904 restraints weight = 29637.486| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.95 r_work: 0.2824 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2826 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2826 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8997 Z= 0.210 Angle : 0.506 7.076 12191 Z= 0.267 Chirality : 0.038 0.151 1390 Planarity : 0.003 0.040 1559 Dihedral : 3.743 18.619 1228 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.01 % Allowed : 11.17 % Favored : 87.82 % 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: 1.01 (0.26), residues: 1119 helix: 2.03 (0.21), residues: 647 sheet: -0.66 (0.68), residues: 65 loop : -1.40 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 573 HIS 0.005 0.001 HIS R 85 PHE 0.019 0.001 PHE C 273 TYR 0.013 0.001 TYR H 38 ARG 0.003 0.000 ARG H 469 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 45 TYR cc_start: 0.7291 (t80) cc_final: 0.7045 (t80) outliers start: 9 outliers final: 6 residues processed: 80 average time/residue: 0.1803 time to fit residues: 22.0208 Evaluate side-chains 72 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain H residue 370 GLU Chi-restraints excluded: chain N residue 31 GLU Chi-restraints excluded: chain N residue 69 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 16 optimal weight: 0.0030 chunk 59 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 115 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 = 0.3516 r_free = 0.3516 target = 0.072855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.051128 restraints weight = 29537.269| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.96 r_work: 0.2830 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8997 Z= 0.175 Angle : 0.482 6.761 12191 Z= 0.252 Chirality : 0.038 0.148 1390 Planarity : 0.003 0.041 1559 Dihedral : 3.679 18.124 1228 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.89 % Allowed : 12.74 % Favored : 86.37 % 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: 1.16 (0.26), residues: 1119 helix: 2.16 (0.21), residues: 646 sheet: -0.52 (0.69), residues: 65 loop : -1.37 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 41 HIS 0.003 0.000 HIS R 85 PHE 0.018 0.001 PHE C 273 TYR 0.012 0.001 TYR H 38 ARG 0.003 0.000 ARG H 469 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 1.000 Fit side-chains REVERT: N 29 ARG cc_start: 0.9207 (mtt90) cc_final: 0.8978 (ttm110) REVERT: N 50 MET cc_start: 0.6667 (mtt) cc_final: 0.5793 (mtt) outliers start: 8 outliers final: 5 residues processed: 83 average time/residue: 0.1778 time to fit residues: 22.6474 Evaluate side-chains 72 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain H residue 370 GLU Chi-restraints excluded: chain H residue 454 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 20 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 68 optimal weight: 20.0000 chunk 40 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 115 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 = 0.3500 r_free = 0.3500 target = 0.072138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.050418 restraints weight = 29189.948| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.91 r_work: 0.2807 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8997 Z= 0.226 Angle : 0.511 7.075 12191 Z= 0.269 Chirality : 0.038 0.151 1390 Planarity : 0.003 0.041 1559 Dihedral : 3.746 18.835 1228 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.45 % Allowed : 14.41 % Favored : 84.13 % 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: 1.15 (0.26), residues: 1119 helix: 2.20 (0.21), residues: 647 sheet: -0.44 (0.71), residues: 65 loop : -1.49 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 573 HIS 0.004 0.001 HIS R 85 PHE 0.015 0.001 PHE C 273 TYR 0.013 0.001 TYR C 214 ARG 0.004 0.000 ARG N 29 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.973 Fit side-chains REVERT: R 32 LEU cc_start: 0.9608 (OUTLIER) cc_final: 0.9365 (tt) REVERT: N 50 MET cc_start: 0.6566 (mtt) cc_final: 0.5380 (mtt) REVERT: N 53 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8220 (pp20) outliers start: 13 outliers final: 9 residues processed: 81 average time/residue: 0.1698 time to fit residues: 20.9359 Evaluate side-chains 76 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 488 ASP Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain H residue 370 GLU Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 23 VAL Chi-restraints excluded: chain N residue 69 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 3 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 91 optimal weight: 0.4980 chunk 94 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 115 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 = 0.3501 r_free = 0.3501 target = 0.072160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.050485 restraints weight = 29142.600| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.92 r_work: 0.2810 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8997 Z= 0.199 Angle : 0.507 7.631 12191 Z= 0.264 Chirality : 0.038 0.150 1390 Planarity : 0.003 0.049 1559 Dihedral : 3.724 18.614 1228 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.68 % Allowed : 14.75 % Favored : 83.58 % 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: 1.20 (0.26), residues: 1119 helix: 2.23 (0.21), residues: 647 sheet: -0.38 (0.72), residues: 65 loop : -1.46 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 41 HIS 0.003 0.001 HIS R 85 PHE 0.013 0.001 PHE C 273 TYR 0.012 0.001 TYR C 214 ARG 0.003 0.000 ARG H 469 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.962 Fit side-chains REVERT: R 32 LEU cc_start: 0.9603 (OUTLIER) cc_final: 0.9368 (tt) REVERT: N 50 MET cc_start: 0.6485 (mtt) cc_final: 0.5656 (mtt) REVERT: N 53 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8290 (pp20) outliers start: 15 outliers final: 10 residues processed: 85 average time/residue: 0.1784 time to fit residues: 22.6390 Evaluate side-chains 77 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 488 ASP Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain H residue 370 GLU Chi-restraints excluded: chain H residue 454 ILE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 7 THR Chi-restraints excluded: chain N residue 69 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 26 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 115 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 = 0.3495 r_free = 0.3495 target = 0.071758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.050310 restraints weight = 29377.903| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.75 r_work: 0.2829 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8997 Z= 0.224 Angle : 0.521 7.066 12191 Z= 0.271 Chirality : 0.038 0.151 1390 Planarity : 0.003 0.041 1559 Dihedral : 3.747 19.059 1228 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.79 % Allowed : 15.08 % Favored : 83.13 % 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: 1.23 (0.26), residues: 1119 helix: 2.26 (0.21), residues: 644 sheet: -0.35 (0.72), residues: 65 loop : -1.45 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 41 HIS 0.003 0.001 HIS R 85 PHE 0.013 0.001 PHE C 202 TYR 0.013 0.001 TYR C 214 ARG 0.003 0.000 ARG C 691 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 1.002 Fit side-chains REVERT: N 50 MET cc_start: 0.6582 (mtt) cc_final: 0.5738 (mtt) outliers start: 16 outliers final: 11 residues processed: 81 average time/residue: 0.1556 time to fit residues: 19.8129 Evaluate side-chains 79 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 488 ASP Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain H residue 370 GLU Chi-restraints excluded: chain H residue 454 ILE Chi-restraints excluded: chain R residue 48 ASP Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 15 ILE Chi-restraints excluded: chain N residue 69 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.0980 chunk 48 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.071630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.051745 restraints weight = 29045.988| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.73 r_work: 0.2833 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2840 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2840 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8997 Z= 0.221 Angle : 0.532 7.084 12191 Z= 0.274 Chirality : 0.038 0.150 1390 Planarity : 0.003 0.042 1559 Dihedral : 3.773 19.081 1228 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.56 % Allowed : 15.42 % Favored : 83.02 % 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: 1.30 (0.26), residues: 1119 helix: 2.27 (0.21), residues: 647 sheet: 0.49 (0.80), residues: 55 loop : -1.45 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 41 HIS 0.003 0.001 HIS R 85 PHE 0.013 0.001 PHE C 202 TYR 0.016 0.001 TYR N 45 ARG 0.003 0.000 ARG H 469 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 1.490 Fit side-chains REVERT: N 6 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7706 (tptm) REVERT: N 11 LYS cc_start: 0.8428 (tptm) cc_final: 0.8057 (mmmt) REVERT: N 50 MET cc_start: 0.6512 (mtt) cc_final: 0.5662 (mtt) outliers start: 14 outliers final: 10 residues processed: 77 average time/residue: 0.2086 time to fit residues: 26.3217 Evaluate side-chains 77 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 488 ASP Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 370 GLU Chi-restraints excluded: chain R residue 48 ASP Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 69 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 63 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 0.3980 chunk 99 optimal weight: 1.9990 chunk 110 optimal weight: 0.2980 chunk 1 optimal weight: 1.9990 chunk 46 optimal weight: 0.0060 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.072466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.052745 restraints weight = 28960.249| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.71 r_work: 0.2864 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2872 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8997 Z= 0.159 Angle : 0.519 9.299 12191 Z= 0.265 Chirality : 0.038 0.149 1390 Planarity : 0.003 0.042 1559 Dihedral : 3.690 18.202 1228 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.01 % Allowed : 16.09 % Favored : 82.91 % 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: 1.36 (0.26), residues: 1119 helix: 2.34 (0.21), residues: 646 sheet: -0.18 (0.72), residues: 65 loop : -1.37 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 41 HIS 0.002 0.000 HIS R 85 PHE 0.012 0.001 PHE C 273 TYR 0.014 0.001 TYR N 45 ARG 0.002 0.000 ARG N 25 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 1.170 Fit side-chains REVERT: N 6 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7695 (tptm) REVERT: N 11 LYS cc_start: 0.8444 (tptm) cc_final: 0.8060 (mmmt) REVERT: N 50 MET cc_start: 0.6434 (mtt) cc_final: 0.5581 (mtt) outliers start: 9 outliers final: 8 residues processed: 77 average time/residue: 0.1699 time to fit residues: 20.3267 Evaluate side-chains 74 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 488 ASP Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain H residue 59 TYR Chi-restraints excluded: chain H residue 370 GLU Chi-restraints excluded: chain R residue 48 ASP Chi-restraints excluded: chain N residue 6 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 74 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 46 optimal weight: 0.0970 chunk 48 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.072191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.052501 restraints weight = 28846.495| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.69 r_work: 0.2857 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8997 Z= 0.181 Angle : 0.521 7.465 12191 Z= 0.267 Chirality : 0.038 0.148 1390 Planarity : 0.003 0.042 1559 Dihedral : 3.678 18.445 1228 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.12 % Allowed : 16.42 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.26), residues: 1119 helix: 2.35 (0.21), residues: 646 sheet: -0.21 (0.72), residues: 65 loop : -1.31 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 41 HIS 0.002 0.001 HIS R 85 PHE 0.012 0.001 PHE C 202 TYR 0.025 0.001 TYR N 45 ARG 0.002 0.000 ARG H 469 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 1.039 Fit side-chains revert: symmetry clash REVERT: N 6 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7715 (tptm) REVERT: N 11 LYS cc_start: 0.8435 (tptm) cc_final: 0.8078 (mmmt) REVERT: N 50 MET cc_start: 0.6450 (mtt) cc_final: 0.5620 (mtt) outliers start: 10 outliers final: 9 residues processed: 78 average time/residue: 0.1950 time to fit residues: 22.7379 Evaluate side-chains 78 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 488 ASP Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain H residue 370 GLU Chi-restraints excluded: chain R residue 48 ASP Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 6 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 85 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 60 optimal weight: 0.2980 chunk 57 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 98 optimal weight: 0.0170 chunk 30 optimal weight: 0.7980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.072631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.053002 restraints weight = 28857.510| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.74 r_work: 0.2869 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2876 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8997 Z= 0.162 Angle : 0.513 7.324 12191 Z= 0.261 Chirality : 0.038 0.149 1390 Planarity : 0.003 0.042 1559 Dihedral : 3.625 17.974 1228 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.34 % Allowed : 16.20 % Favored : 82.46 % 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: 1.46 (0.26), residues: 1119 helix: 2.40 (0.21), residues: 646 sheet: -0.35 (0.74), residues: 59 loop : -1.24 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 41 HIS 0.002 0.000 HIS R 85 PHE 0.012 0.001 PHE C 273 TYR 0.014 0.001 TYR N 45 ARG 0.002 0.000 ARG H 207 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5032.12 seconds wall clock time: 88 minutes 26.23 seconds (5306.23 seconds total)