Starting phenix.real_space_refine on Tue Mar 3 21:53:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oni_12995/03_2026/7oni_12995.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oni_12995/03_2026/7oni_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_2026/7oni_12995.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oni_12995/03_2026/7oni_12995.map" model { file = "/net/cci-nas-00/data/ceres_data/7oni_12995/03_2026/7oni_12995.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oni_12995/03_2026/7oni_12995.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ARG:plan': 11, 'GLU:plan': 23, 'ASN:plan1': 2, 'GLN:plan1': 5, 'ASP:plan': 6, 'PHE:plan': 1} 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: {'GLU:plan': 9, 'GLN:plan1': 10, 'ASP:plan': 3, 'HIS:plan': 3, 'PHE:plan': 3, 'ARG:plan': 5, 'ASN:plan1': 1} 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: {'GLU:plan': 3, 'GLN:plan1': 1, '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: 2.10, per 1000 atoms: 0.24 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: 0.74 Conformation dependent library (CDL) restraints added in 334.8 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: 0.28 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: 1.40 Time building geometry restraints manager: 0.99 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: 6.890 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: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.600 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.090 ------------------------------------------------------------------------------- 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 0.107 9026 Z= 0.180 Angle : 0.600 11.029 12221 Z= 0.299 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (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 ARG 0.003 0.000 ARG H 482 TYR 0.018 0.001 TYR C 184 PHE 0.008 0.001 PHE H 256 TRP 0.009 0.001 TRP R 41 HIS 0.002 0.000 HIS R 85 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8997) covalent geometry : angle 0.53487 (12191) hydrogen bonds : bond 0.15401 ( 509) hydrogen bonds : angle 5.37595 ( 1494) metal coordination : bond 0.02233 ( 28) metal coordination : angle 5.52906 ( 30) Misc. bond : bond 0.10683 ( 1) *********************** 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 : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.0742 time to fit residues: 10.2812 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 : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.0470 chunk 106 optimal weight: 6.9990 overall best weight: 1.0682 ------------------------------------------------------------------------------- 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 = 0.3497 r_free = 0.3497 target = 0.071986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.050086 restraints weight = 29530.362| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.95 r_work: 0.2800 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2803 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 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 = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9026 Z= 0.189 Angle : 0.571 7.576 12221 Z= 0.294 Chirality : 0.040 0.153 1390 Planarity : 0.003 0.044 1559 Dihedral : 3.963 19.356 1228 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.45 % Allowed : 8.38 % Favored : 91.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.26), residues: 1119 helix: 1.87 (0.21), residues: 645 sheet: -0.78 (0.67), residues: 64 loop : -1.41 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 469 TYR 0.015 0.001 TYR H 38 PHE 0.021 0.002 PHE C 273 TRP 0.013 0.001 TRP C 573 HIS 0.007 0.001 HIS R 85 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 8997) covalent geometry : angle 0.55424 (12191) hydrogen bonds : bond 0.04943 ( 509) hydrogen bonds : angle 4.32489 ( 1494) metal coordination : bond 0.01153 ( 28) metal coordination : angle 2.85535 ( 30) Misc. bond : bond 0.00092 ( 1) *********************** 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 79 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.367 Fit side-chains REVERT: N 45 TYR cc_start: 0.7337 (t80) cc_final: 0.7133 (t80) REVERT: N 52 ASP cc_start: 0.7697 (t0) cc_final: 0.7402 (t0) outliers start: 4 outliers final: 3 residues processed: 77 average time/residue: 0.0789 time to fit residues: 9.2662 Evaluate side-chains 68 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain H residue 370 GLU Chi-restraints excluded: chain N residue 7 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 96 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 86 optimal weight: 0.2980 chunk 65 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 94 optimal weight: 0.3980 chunk 46 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3508 r_free = 0.3508 target = 0.072536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.050825 restraints weight = 29346.179| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.93 r_work: 0.2821 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 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 = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9026 Z= 0.126 Angle : 0.512 7.082 12221 Z= 0.262 Chirality : 0.038 0.147 1390 Planarity : 0.003 0.042 1559 Dihedral : 3.807 18.539 1228 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.89 % Allowed : 11.17 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.26), residues: 1119 helix: 1.98 (0.21), residues: 647 sheet: -0.53 (0.69), residues: 64 loop : -1.48 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 469 TYR 0.013 0.001 TYR H 38 PHE 0.015 0.001 PHE C 202 TRP 0.010 0.001 TRP R 41 HIS 0.003 0.001 HIS R 85 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8997) covalent geometry : angle 0.49907 (12191) hydrogen bonds : bond 0.04201 ( 509) hydrogen bonds : angle 3.98411 ( 1494) metal coordination : bond 0.00587 ( 28) metal coordination : angle 2.38874 ( 30) Misc. bond : bond 0.00002 ( 1) *********************** 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 81 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.342 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 78 average time/residue: 0.0783 time to fit residues: 9.2445 Evaluate side-chains 67 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain H residue 370 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 53 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 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 = 0.3493 r_free = 0.3493 target = 0.071894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.050120 restraints weight = 29865.910| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.96 r_work: 0.2798 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 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 = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9026 Z= 0.153 Angle : 0.526 7.078 12221 Z= 0.270 Chirality : 0.039 0.172 1390 Planarity : 0.003 0.042 1559 Dihedral : 3.810 18.990 1228 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.12 % Allowed : 12.63 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.26), residues: 1119 helix: 2.08 (0.21), residues: 645 sheet: -0.48 (0.70), residues: 65 loop : -1.52 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 469 TYR 0.013 0.001 TYR C 214 PHE 0.015 0.001 PHE C 202 TRP 0.009 0.001 TRP C 573 HIS 0.003 0.001 HIS R 85 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 8997) covalent geometry : angle 0.51262 (12191) hydrogen bonds : bond 0.04383 ( 509) hydrogen bonds : angle 3.92986 ( 1494) metal coordination : bond 0.00738 ( 28) metal coordination : angle 2.43731 ( 30) Misc. bond : bond 0.00024 ( 1) *********************** 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: 10 poor density : 75 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 774 ASN cc_start: 0.6806 (m-40) cc_final: 0.6458 (p0) outliers start: 10 outliers final: 6 residues processed: 83 average time/residue: 0.0754 time to fit residues: 9.3370 Evaluate side-chains 75 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 C residue 647 VAL Chi-restraints excluded: chain H residue 370 GLU Chi-restraints excluded: chain N residue 7 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 95 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 9 optimal weight: 0.1980 chunk 85 optimal weight: 0.9980 chunk 34 optimal weight: 0.0870 chunk 4 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.072554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.050952 restraints weight = 29575.989| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.95 r_work: 0.2824 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 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 = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9026 Z= 0.115 Angle : 0.500 6.859 12221 Z= 0.258 Chirality : 0.038 0.194 1390 Planarity : 0.003 0.042 1559 Dihedral : 3.715 18.147 1228 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.56 % Allowed : 14.53 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.26), residues: 1119 helix: 2.20 (0.21), residues: 647 sheet: -0.42 (0.71), residues: 65 loop : -1.49 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 469 TYR 0.011 0.001 TYR C 214 PHE 0.013 0.001 PHE C 202 TRP 0.010 0.001 TRP R 41 HIS 0.002 0.000 HIS R 85 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 8997) covalent geometry : angle 0.48845 (12191) hydrogen bonds : bond 0.03902 ( 509) hydrogen bonds : angle 3.77570 ( 1494) metal coordination : bond 0.00495 ( 28) metal coordination : angle 2.21890 ( 30) Misc. bond : bond 0.00009 ( 1) *********************** 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 92 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: R 32 LEU cc_start: 0.9614 (OUTLIER) cc_final: 0.9363 (tt) outliers start: 14 outliers final: 7 residues processed: 88 average time/residue: 0.0718 time to fit residues: 9.3870 Evaluate side-chains 74 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 48 ASP Chi-restraints excluded: chain N residue 5 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 33 optimal weight: 1.9990 chunk 70 optimal weight: 20.0000 chunk 81 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 54 optimal weight: 0.0970 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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** R 96 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.071556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.050067 restraints weight = 29816.189| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.77 r_work: 0.2819 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2825 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 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 = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2825 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9026 Z= 0.170 Angle : 0.553 7.184 12221 Z= 0.286 Chirality : 0.039 0.232 1390 Planarity : 0.003 0.042 1559 Dihedral : 3.805 19.202 1228 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.01 % Allowed : 15.08 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.26), residues: 1119 helix: 2.17 (0.21), residues: 645 sheet: -0.40 (0.73), residues: 65 loop : -1.52 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 29 TYR 0.013 0.001 TYR C 214 PHE 0.022 0.001 PHE C 273 TRP 0.008 0.001 TRP C 573 HIS 0.003 0.001 HIS R 85 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 8997) covalent geometry : angle 0.54115 (12191) hydrogen bonds : bond 0.04447 ( 509) hydrogen bonds : angle 3.90112 ( 1494) metal coordination : bond 0.00820 ( 28) metal coordination : angle 2.38800 ( 30) Misc. bond : bond 0.00014 ( 1) *********************** 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 93 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 774 ASN cc_start: 0.6755 (m-40) cc_final: 0.6543 (p0) REVERT: R 32 LEU cc_start: 0.9655 (OUTLIER) cc_final: 0.9435 (tt) REVERT: N 6 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7903 (tptm) outliers start: 18 outliers final: 10 residues processed: 90 average time/residue: 0.0769 time to fit residues: 10.2269 Evaluate side-chains 78 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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 32 LEU Chi-restraints excluded: chain R residue 48 ASP Chi-restraints excluded: chain N residue 6 LYS 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 40 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 104 optimal weight: 7.9990 chunk 19 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3487 r_free = 0.3487 target = 0.071527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.050066 restraints weight = 29738.367| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.75 r_work: 0.2820 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2826 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 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 = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.045 | | 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: 0.8660 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9026 Z= 0.157 Angle : 0.552 7.462 12221 Z= 0.285 Chirality : 0.039 0.242 1390 Planarity : 0.003 0.042 1559 Dihedral : 3.822 19.276 1228 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.46 % Allowed : 15.08 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.26), residues: 1119 helix: 2.19 (0.21), residues: 645 sheet: -0.50 (0.71), residues: 65 loop : -1.51 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 482 TYR 0.013 0.001 TYR C 214 PHE 0.019 0.001 PHE C 273 TRP 0.009 0.001 TRP R 41 HIS 0.003 0.001 HIS R 85 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 8997) covalent geometry : angle 0.54014 (12191) hydrogen bonds : bond 0.04366 ( 509) hydrogen bonds : angle 3.86652 ( 1494) metal coordination : bond 0.00721 ( 28) metal coordination : angle 2.34514 ( 30) Misc. bond : bond 0.00010 ( 1) *********************** 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 94 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 32 LEU cc_start: 0.9650 (OUTLIER) cc_final: 0.9440 (tt) REVERT: N 6 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7869 (tptm) REVERT: N 50 MET cc_start: 0.5798 (OUTLIER) cc_final: 0.5220 (mtm) outliers start: 22 outliers final: 14 residues processed: 90 average time/residue: 0.0751 time to fit residues: 10.2857 Evaluate side-chains 83 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 404 CYS 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 59 TYR 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 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 7 THR Chi-restraints excluded: chain N residue 50 MET 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 109 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 68 optimal weight: 20.0000 chunk 71 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3490 r_free = 0.3490 target = 0.071520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.050264 restraints weight = 29158.932| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.71 r_work: 0.2831 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- 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: 0.8657 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9026 Z= 0.158 Angle : 0.557 8.321 12221 Z= 0.287 Chirality : 0.039 0.202 1390 Planarity : 0.003 0.042 1559 Dihedral : 3.827 19.190 1228 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.23 % Allowed : 15.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.26), residues: 1119 helix: 2.18 (0.21), residues: 645 sheet: -0.44 (0.77), residues: 59 loop : -1.42 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 29 TYR 0.013 0.001 TYR C 214 PHE 0.018 0.001 PHE C 273 TRP 0.009 0.001 TRP R 41 HIS 0.003 0.001 HIS R 85 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 8997) covalent geometry : angle 0.54476 (12191) hydrogen bonds : bond 0.04380 ( 509) hydrogen bonds : angle 3.90065 ( 1494) metal coordination : bond 0.00708 ( 28) metal coordination : angle 2.36974 ( 30) Misc. bond : bond 0.00012 ( 1) *********************** 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 88 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 32 LEU cc_start: 0.9640 (OUTLIER) cc_final: 0.9430 (tt) REVERT: N 6 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7898 (tptm) REVERT: N 50 MET cc_start: 0.5712 (OUTLIER) cc_final: 0.5195 (mtm) outliers start: 20 outliers final: 12 residues processed: 83 average time/residue: 0.0792 time to fit residues: 9.9370 Evaluate side-chains 80 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 404 CYS 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 H residue 454 ILE Chi-restraints excluded: chain R residue 32 LEU 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 31 GLU Chi-restraints excluded: chain N residue 50 MET 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 62 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 76 optimal weight: 0.7980 chunk 68 optimal weight: 20.0000 chunk 86 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3496 r_free = 0.3496 target = 0.071776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.050582 restraints weight = 28918.886| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.71 r_work: 0.2840 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 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 = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9026 Z= 0.137 Angle : 0.556 7.888 12221 Z= 0.284 Chirality : 0.039 0.156 1390 Planarity : 0.003 0.042 1559 Dihedral : 3.807 18.953 1228 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.12 % Allowed : 15.53 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.26), residues: 1119 helix: 2.20 (0.21), residues: 648 sheet: -0.49 (0.76), residues: 59 loop : -1.43 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 261 TYR 0.012 0.001 TYR C 214 PHE 0.017 0.001 PHE C 273 TRP 0.010 0.001 TRP R 41 HIS 0.003 0.001 HIS R 85 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8997) covalent geometry : angle 0.54479 (12191) hydrogen bonds : bond 0.04149 ( 509) hydrogen bonds : angle 3.83328 ( 1494) metal coordination : bond 0.00577 ( 28) metal coordination : angle 2.27296 ( 30) Misc. bond : bond 0.00009 ( 1) *********************** 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 86 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 32 LEU cc_start: 0.9637 (OUTLIER) cc_final: 0.9436 (tt) REVERT: N 6 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7920 (tptm) REVERT: N 50 MET cc_start: 0.5598 (OUTLIER) cc_final: 0.5213 (mtm) outliers start: 19 outliers final: 15 residues processed: 81 average time/residue: 0.0668 time to fit residues: 8.1464 Evaluate side-chains 82 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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 404 CYS 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 59 TYR 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 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 28 GLU Chi-restraints excluded: chain N residue 31 GLU Chi-restraints excluded: chain N residue 50 MET Chi-restraints excluded: chain N residue 69 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 79 optimal weight: 0.9990 chunk 111 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 17 optimal weight: 0.0570 chunk 108 optimal weight: 0.0870 chunk 61 optimal weight: 1.9990 chunk 70 optimal weight: 0.0270 chunk 101 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 99 optimal weight: 0.1980 chunk 96 optimal weight: 0.8980 overall best weight: 0.1934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 527 ASN ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 477 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.073387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.053800 restraints weight = 28790.745| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.75 r_work: 0.2895 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2902 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2902 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 9026 Z= 0.104 Angle : 0.532 8.594 12221 Z= 0.270 Chirality : 0.038 0.175 1390 Planarity : 0.003 0.042 1559 Dihedral : 3.641 17.044 1228 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.34 % Allowed : 16.54 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.26), residues: 1119 helix: 2.33 (0.21), residues: 647 sheet: -0.48 (0.75), residues: 59 loop : -1.32 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 714 TYR 0.010 0.001 TYR N 45 PHE 0.017 0.001 PHE C 273 TRP 0.016 0.001 TRP R 41 HIS 0.002 0.000 HIS C 572 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 8997) covalent geometry : angle 0.52405 (12191) hydrogen bonds : bond 0.03419 ( 509) hydrogen bonds : angle 3.68632 ( 1494) metal coordination : bond 0.00348 ( 28) metal coordination : angle 1.97690 ( 30) Misc. bond : bond 0.00003 ( 1) ********************** 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 88 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 3 ILE cc_start: 0.8003 (mm) cc_final: 0.7769 (mm) REVERT: N 6 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7852 (tptm) REVERT: N 11 LYS cc_start: 0.8389 (tptm) cc_final: 0.8053 (mmmt) outliers start: 12 outliers final: 8 residues processed: 84 average time/residue: 0.0819 time to fit residues: 10.1433 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 : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 454 ILE Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 28 GLU Chi-restraints excluded: chain N residue 31 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 17 optimal weight: 0.1980 chunk 8 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 27 optimal weight: 0.3980 chunk 59 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 38 optimal weight: 0.3980 chunk 53 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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** ** N 41 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 = 0.072426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.052677 restraints weight = 28631.919| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.71 r_work: 0.2860 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 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 = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9026 Z= 0.128 Angle : 0.558 8.958 12221 Z= 0.280 Chirality : 0.038 0.177 1390 Planarity : 0.003 0.041 1559 Dihedral : 3.685 18.046 1228 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.23 % Allowed : 16.20 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.26), residues: 1119 helix: 2.35 (0.21), residues: 647 sheet: -0.46 (0.76), residues: 59 loop : -1.29 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 207 TYR 0.014 0.001 TYR N 45 PHE 0.016 0.001 PHE C 273 TRP 0.009 0.001 TRP R 41 HIS 0.002 0.000 HIS R 85 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 8997) covalent geometry : angle 0.54883 (12191) hydrogen bonds : bond 0.03803 ( 509) hydrogen bonds : angle 3.73673 ( 1494) metal coordination : bond 0.00505 ( 28) metal coordination : angle 2.13586 ( 30) Misc. bond : bond 0.00009 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2349.11 seconds wall clock time: 40 minutes 48.05 seconds (2448.05 seconds total)