Starting phenix.real_space_refine on Sat Jul 26 22:42:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oni_12995/07_2025/7oni_12995.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oni_12995/07_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_12995/07_2025/7oni_12995.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oni_12995/07_2025/7oni_12995.map" model { file = "/net/cci-nas-00/data/ceres_data/7oni_12995/07_2025/7oni_12995.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oni_12995/07_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 6.61, per 1000 atoms: 0.75 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: 2.45 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.98 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: 2.64 Time building geometry restraints manager: 2.88 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: 173.940 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: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.610 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 204.060 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.15401 ( 509) hydrogen bonds : angle 5.37595 ( 1494) metal coordination : bond 0.02233 ( 28) metal coordination : angle 5.52906 ( 30) covalent geometry : bond 0.00267 ( 8997) covalent geometry : angle 0.53487 (12191) 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 : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1723 time to fit residues: 23.5720 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 : 1.053 ------------------------------------------------------------------------------- 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: 0.9980 overall best weight: 0.4576 ------------------------------------------------------------------------------- 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 = 0.3536 r_free = 0.3536 target = 0.073720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.052178 restraints weight = 29182.636| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.91 r_work: 0.2862 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 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 = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.0935 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= 0.121 Angle : 0.517 6.951 12221 Z= 0.267 Chirality : 0.038 0.146 1390 Planarity : 0.003 0.043 1559 Dihedral : 3.772 17.877 1228 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.45 % Allowed : 7.49 % Favored : 92.07 % 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: 0.99 (0.26), residues: 1119 helix: 1.96 (0.21), residues: 646 sheet: -0.76 (0.67), residues: 64 loop : -1.28 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 573 HIS 0.004 0.001 HIS R 85 PHE 0.020 0.001 PHE C 273 TYR 0.012 0.001 TYR H 38 ARG 0.004 0.000 ARG C 167 Details of bonding type rmsd hydrogen bonds : bond 0.04318 ( 509) hydrogen bonds : angle 4.22156 ( 1494) metal coordination : bond 0.00666 ( 28) metal coordination : angle 2.48499 ( 30) covalent geometry : bond 0.00258 ( 8997) covalent geometry : angle 0.50270 (12191) 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 81 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.989 Fit side-chains revert: symmetry clash REVERT: N 52 ASP cc_start: 0.7656 (t0) cc_final: 0.7364 (t0) outliers start: 4 outliers final: 3 residues processed: 79 average time/residue: 0.1727 time to fit residues: 20.7332 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 : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 655 ASN Chi-restraints excluded: chain H residue 370 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 45 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 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 = 0.3516 r_free = 0.3516 target = 0.072842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.051144 restraints weight = 29661.924| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.95 r_work: 0.2831 rms_B_bonded: 3.59 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: 0.8601 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9026 Z= 0.135 Angle : 0.504 6.990 12221 Z= 0.260 Chirality : 0.038 0.148 1390 Planarity : 0.003 0.041 1559 Dihedral : 3.708 18.271 1228 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.01 % Allowed : 10.61 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.26), residues: 1119 helix: 2.03 (0.21), residues: 646 sheet: -0.67 (0.67), residues: 65 loop : -1.38 (0.31), residues: 408 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 Details of bonding type rmsd hydrogen bonds : bond 0.04199 ( 509) hydrogen bonds : angle 3.98347 ( 1494) metal coordination : bond 0.00635 ( 28) metal coordination : angle 2.35862 ( 30) covalent geometry : bond 0.00297 ( 8997) covalent geometry : angle 0.49123 (12191) Misc. bond : bond 0.00014 ( 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 79 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 45 TYR cc_start: 0.7256 (t80) cc_final: 0.7010 (t80) outliers start: 9 outliers final: 5 residues processed: 75 average time/residue: 0.1809 time to fit residues: 20.6700 Evaluate side-chains 71 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 1.086 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 31 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 37 optimal weight: 0.7980 chunk 40 optimal weight: 0.0980 chunk 60 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 24 optimal weight: 0.4980 chunk 83 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.072884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.051235 restraints weight = 29555.069| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.94 r_work: 0.2834 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2837 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 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 = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2837 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1401 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= 0.119 Angle : 0.490 6.794 12221 Z= 0.250 Chirality : 0.037 0.149 1390 Planarity : 0.003 0.041 1559 Dihedral : 3.658 18.145 1228 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.78 % Allowed : 12.40 % Favored : 86.82 % 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: 1.12 (0.26), residues: 1119 helix: 2.13 (0.21), residues: 647 sheet: -0.52 (0.69), residues: 65 loop : -1.39 (0.31), residues: 407 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 0.015 0.001 PHE C 273 TYR 0.012 0.001 TYR H 38 ARG 0.002 0.000 ARG H 469 Details of bonding type rmsd hydrogen bonds : bond 0.03978 ( 509) hydrogen bonds : angle 3.84104 ( 1494) metal coordination : bond 0.00540 ( 28) metal coordination : angle 2.27012 ( 30) covalent geometry : bond 0.00265 ( 8997) covalent geometry : angle 0.47757 (12191) Misc. bond : bond 0.00009 ( 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 83 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 1.004 Fit side-chains revert: symmetry clash REVERT: N 50 MET cc_start: 0.6709 (mtt) cc_final: 0.5938 (mtt) outliers start: 7 outliers final: 6 residues processed: 81 average time/residue: 0.1729 time to fit residues: 21.4443 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 : 1.128 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain N residue 31 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 20 optimal weight: 0.9980 chunk 74 optimal weight: 0.0000 chunk 15 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 68 optimal weight: 20.0000 chunk 40 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- 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 = 0.3517 r_free = 0.3517 target = 0.072912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.051264 restraints weight = 29294.834| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.92 r_work: 0.2835 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2837 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 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 = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2837 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9026 Z= 0.119 Angle : 0.493 6.819 12221 Z= 0.253 Chirality : 0.037 0.149 1390 Planarity : 0.003 0.041 1559 Dihedral : 3.637 18.056 1228 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.34 % Allowed : 14.08 % Favored : 84.58 % 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: 1.21 (0.26), residues: 1119 helix: 2.22 (0.21), residues: 647 sheet: -0.45 (0.70), residues: 65 loop : -1.40 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 41 HIS 0.002 0.000 HIS R 85 PHE 0.020 0.001 PHE C 273 TYR 0.011 0.001 TYR C 214 ARG 0.004 0.000 ARG N 29 Details of bonding type rmsd hydrogen bonds : bond 0.03893 ( 509) hydrogen bonds : angle 3.76310 ( 1494) metal coordination : bond 0.00511 ( 28) metal coordination : angle 2.17217 ( 30) covalent geometry : bond 0.00261 ( 8997) covalent geometry : angle 0.48128 (12191) Misc. bond : bond 0.00012 ( 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 87 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 1.006 Fit side-chains revert: symmetry clash REVERT: R 32 LEU cc_start: 0.9607 (OUTLIER) cc_final: 0.9369 (tt) REVERT: N 50 MET cc_start: 0.6507 (mtt) cc_final: 0.5689 (mtt) REVERT: N 53 GLU cc_start: 0.8439 (tm-30) cc_final: 0.8237 (pp20) outliers start: 12 outliers final: 8 residues processed: 85 average time/residue: 0.1755 time to fit residues: 22.6467 Evaluate side-chains 76 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 H residue 454 ILE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain N residue 31 GLU 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: 0.7980 chunk 69 optimal weight: 0.0980 chunk 90 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 0.1980 chunk 29 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3519 r_free = 0.3519 target = 0.073051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.051332 restraints weight = 29173.859| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.93 r_work: 0.2838 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- 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: 0.8593 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9026 Z= 0.114 Angle : 0.496 7.240 12221 Z= 0.254 Chirality : 0.037 0.149 1390 Planarity : 0.003 0.041 1559 Dihedral : 3.637 17.788 1228 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.68 % Allowed : 14.41 % 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 (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: 1.34 (0.26), residues: 1119 helix: 2.32 (0.21), residues: 646 sheet: -0.44 (0.70), residues: 65 loop : -1.32 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 41 HIS 0.002 0.001 HIS R 85 PHE 0.018 0.001 PHE C 273 TYR 0.011 0.001 TYR N 45 ARG 0.002 0.000 ARG H 469 Details of bonding type rmsd hydrogen bonds : bond 0.03735 ( 509) hydrogen bonds : angle 3.71317 ( 1494) metal coordination : bond 0.00462 ( 28) metal coordination : angle 2.08411 ( 30) covalent geometry : bond 0.00249 ( 8997) covalent geometry : angle 0.48549 (12191) Misc. bond : bond 0.00011 ( 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 87 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 1.004 Fit side-chains REVERT: C 514 HIS cc_start: 0.7416 (t70) cc_final: 0.7166 (t70) REVERT: R 32 LEU cc_start: 0.9600 (OUTLIER) cc_final: 0.9376 (tt) REVERT: N 28 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8819 (mm-30) REVERT: N 50 MET cc_start: 0.6399 (mtt) cc_final: 0.5558 (mtt) outliers start: 15 outliers final: 8 residues processed: 84 average time/residue: 0.1901 time to fit residues: 24.2844 Evaluate side-chains 76 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 C residue 751 LYS Chi-restraints excluded: chain H residue 454 ILE Chi-restraints excluded: chain R residue 32 LEU 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: 0.9990 chunk 80 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 27 optimal weight: 0.0570 chunk 44 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 overall best weight: 0.6698 ------------------------------------------------------------------------------- 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 = 0.3504 r_free = 0.3504 target = 0.072393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.050591 restraints weight = 29450.687| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.93 r_work: 0.2815 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2819 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 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 = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2819 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9026 Z= 0.133 Angle : 0.522 7.445 12221 Z= 0.266 Chirality : 0.038 0.150 1390 Planarity : 0.003 0.041 1559 Dihedral : 3.662 18.320 1228 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.56 % Allowed : 14.75 % Favored : 83.69 % 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: 1.33 (0.26), residues: 1119 helix: 2.33 (0.21), residues: 646 sheet: -0.43 (0.70), residues: 65 loop : -1.36 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 573 HIS 0.003 0.001 HIS R 85 PHE 0.016 0.001 PHE C 273 TYR 0.014 0.001 TYR N 45 ARG 0.003 0.000 ARG N 29 Details of bonding type rmsd hydrogen bonds : bond 0.03979 ( 509) hydrogen bonds : angle 3.73459 ( 1494) metal coordination : bond 0.00595 ( 28) metal coordination : angle 2.21298 ( 30) covalent geometry : bond 0.00301 ( 8997) covalent geometry : angle 0.51082 (12191) Misc. bond : bond 0.00014 ( 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 82 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 1.545 Fit side-chains REVERT: C 514 HIS cc_start: 0.7571 (t70) cc_final: 0.7241 (t70) REVERT: R 32 LEU cc_start: 0.9602 (OUTLIER) cc_final: 0.9371 (tt) REVERT: N 6 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7691 (tptm) REVERT: N 40 GLN cc_start: 0.8531 (mt0) cc_final: 0.8100 (mt0) REVERT: N 50 MET cc_start: 0.6452 (mtt) cc_final: 0.5545 (mtt) outliers start: 14 outliers final: 9 residues processed: 80 average time/residue: 0.2386 time to fit residues: 30.2524 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 : 1.617 ------------------------------------------------------------------------------- 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 C residue 751 LYS 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 69 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.0670 chunk 48 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.071637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.050162 restraints weight = 29804.089| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.75 r_work: 0.2823 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2828 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 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 = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9026 Z= 0.164 Angle : 0.551 7.078 12221 Z= 0.283 Chirality : 0.039 0.151 1390 Planarity : 0.003 0.041 1559 Dihedral : 3.773 19.283 1228 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % 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: 1.32 (0.26), residues: 1119 helix: 2.28 (0.21), residues: 647 sheet: 0.26 (0.77), residues: 55 loop : -1.41 (0.29), residues: 417 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 0.015 0.001 TYR N 45 ARG 0.003 0.000 ARG H 469 Details of bonding type rmsd hydrogen bonds : bond 0.04423 ( 509) hydrogen bonds : angle 3.85149 ( 1494) metal coordination : bond 0.00807 ( 28) metal coordination : angle 2.38344 ( 30) covalent geometry : bond 0.00377 ( 8997) covalent geometry : angle 0.53888 (12191) Misc. bond : bond 0.00020 ( 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 81 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 2.199 Fit side-chains revert: symmetry clash REVERT: N 6 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7754 (tptm) REVERT: N 11 LYS cc_start: 0.8450 (tptm) cc_final: 0.8077 (mmmt) REVERT: N 39 GLN cc_start: 0.9231 (mp10) cc_final: 0.8861 (pp30) REVERT: N 50 MET cc_start: 0.6548 (mtt) cc_final: 0.5660 (mtt) outliers start: 15 outliers final: 9 residues processed: 78 average time/residue: 0.2606 time to fit residues: 31.6826 Evaluate side-chains 74 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 1.310 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 62 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 99 optimal weight: 0.0970 chunk 110 optimal weight: 0.0770 chunk 1 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 overall best weight: 0.4736 ------------------------------------------------------------------------------- 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 = 0.3514 r_free = 0.3514 target = 0.072586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.052814 restraints weight = 29014.348| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.72 r_work: 0.2864 rms_B_bonded: 3.34 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: 0.8623 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9026 Z= 0.116 Angle : 0.541 10.228 12221 Z= 0.273 Chirality : 0.038 0.150 1390 Planarity : 0.003 0.042 1559 Dihedral : 3.693 18.202 1228 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.12 % Allowed : 15.31 % 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: 1.35 (0.26), residues: 1119 helix: 2.35 (0.21), residues: 646 sheet: -0.44 (0.69), residues: 65 loop : -1.35 (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 0.015 0.001 PHE C 273 TYR 0.024 0.001 TYR N 45 ARG 0.002 0.000 ARG H 469 Details of bonding type rmsd hydrogen bonds : bond 0.03820 ( 509) hydrogen bonds : angle 3.71363 ( 1494) metal coordination : bond 0.00454 ( 28) metal coordination : angle 2.10016 ( 30) covalent geometry : bond 0.00256 ( 8997) covalent geometry : angle 0.53199 (12191) Misc. bond : bond 0.00027 ( 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 78 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 1.037 Fit side-chains revert: symmetry clash REVERT: N 6 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7795 (tptm) REVERT: N 11 LYS cc_start: 0.8432 (tptm) cc_final: 0.8096 (mmmt) REVERT: N 50 MET cc_start: 0.6469 (mtt) cc_final: 0.5591 (mtt) outliers start: 10 outliers final: 8 residues processed: 76 average time/residue: 0.1878 time to fit residues: 21.8460 Evaluate side-chains 73 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.988 ------------------------------------------------------------------------------- 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 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 74 optimal weight: 0.9980 chunk 12 optimal weight: 0.0770 chunk 25 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 46 optimal weight: 0.3980 chunk 48 optimal weight: 0.7980 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 = 0.3514 r_free = 0.3514 target = 0.072512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.052752 restraints weight = 28841.645| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.73 r_work: 0.2861 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 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 = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9026 Z= 0.120 Angle : 0.534 7.412 12221 Z= 0.271 Chirality : 0.038 0.154 1390 Planarity : 0.003 0.041 1559 Dihedral : 3.647 18.161 1228 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.12 % Allowed : 15.31 % 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: 1.37 (0.26), residues: 1119 helix: 2.36 (0.21), residues: 646 sheet: -0.69 (0.72), residues: 59 loop : -1.28 (0.30), residues: 414 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 0.014 0.001 PHE C 273 TYR 0.014 0.001 TYR N 45 ARG 0.002 0.000 ARG H 469 Details of bonding type rmsd hydrogen bonds : bond 0.03852 ( 509) hydrogen bonds : angle 3.68374 ( 1494) metal coordination : bond 0.00472 ( 28) metal coordination : angle 2.11351 ( 30) covalent geometry : bond 0.00267 ( 8997) covalent geometry : angle 0.52472 (12191) Misc. bond : bond 0.00016 ( 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 77 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.980 Fit side-chains revert: symmetry clash REVERT: N 6 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7849 (tptm) REVERT: N 11 LYS cc_start: 0.8438 (tptm) cc_final: 0.8133 (mmmt) REVERT: N 50 MET cc_start: 0.6615 (mtt) cc_final: 0.5866 (mtt) outliers start: 10 outliers final: 8 residues processed: 75 average time/residue: 0.1942 time to fit residues: 21.6944 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 : 1.078 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 56 optimal weight: 0.7980 chunk 85 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3503 r_free = 0.3503 target = 0.072015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.052194 restraints weight = 28852.668| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.75 r_work: 0.2844 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2851 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 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 = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2851 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9026 Z= 0.138 Angle : 0.555 7.426 12221 Z= 0.280 Chirality : 0.038 0.150 1390 Planarity : 0.003 0.041 1559 Dihedral : 3.680 18.765 1228 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.12 % Allowed : 15.31 % 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: 1.38 (0.26), residues: 1119 helix: 2.34 (0.21), residues: 646 sheet: -0.64 (0.72), residues: 59 loop : -1.25 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 573 HIS 0.003 0.001 HIS R 85 PHE 0.014 0.001 PHE C 273 TYR 0.015 0.001 TYR N 45 ARG 0.002 0.000 ARG H 207 Details of bonding type rmsd hydrogen bonds : bond 0.04060 ( 509) hydrogen bonds : angle 3.72649 ( 1494) metal coordination : bond 0.00608 ( 28) metal coordination : angle 2.22509 ( 30) covalent geometry : bond 0.00313 ( 8997) covalent geometry : angle 0.54455 (12191) Misc. bond : bond 0.00014 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5339.64 seconds wall clock time: 95 minutes 31.63 seconds (5731.63 seconds total)