Starting phenix.real_space_refine on Sun May 18 10:16:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cdk_16576/05_2025/8cdk_16576.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cdk_16576/05_2025/8cdk_16576.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cdk_16576/05_2025/8cdk_16576.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cdk_16576/05_2025/8cdk_16576.map" model { file = "/net/cci-nas-00/data/ceres_data/8cdk_16576/05_2025/8cdk_16576.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cdk_16576/05_2025/8cdk_16576.cif" } resolution = 3.32 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= 0.002 sd= 0.032 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 3 6.06 5 S 92 5.16 5 C 10728 2.51 5 N 2964 2.21 5 O 3118 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16905 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 5544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 5544 Classifications: {'peptide': 718} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 12, 'TRANS': 705} Chain breaks: 4 Unresolved non-hydrogen bonds: 336 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 280 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 15, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 194 Chain: "D" Number of atoms: 8329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1141, 8329 Classifications: {'peptide': 1141} Incomplete info: {'truncation_to_alanine': 149} Link IDs: {'PTRANS': 52, 'TRANS': 1088} Chain breaks: 5 Unresolved non-hydrogen bonds: 566 Unresolved non-hydrogen angles: 678 Unresolved non-hydrogen dihedrals: 459 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 25, 'GLU:plan': 50, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 357 Chain: "R" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 645 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "S" Number of atoms: 765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 765 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain breaks: 2 Unresolved non-hydrogen bonds: 320 Unresolved non-hydrogen angles: 404 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 2, 'ASN:plan1': 6, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 13, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 178 Chain: "F" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 1619 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 267} Link IDs: {'PTRANS': 13, 'TRANS': 299} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 899 Unresolved non-hydrogen angles: 1153 Unresolved non-hydrogen dihedrals: 727 Unresolved non-hydrogen chiralities: 100 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 10, 'TYR:plan': 4, 'ASN:plan1': 14, 'TRP:plan': 2, 'ASP:plan': 16, 'PHE:plan': 13, 'GLU:plan': 15, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 463 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 14033 SG CYS R 42 131.778 57.666 47.797 1.00 85.58 S ATOM 14052 SG CYS R 45 134.204 55.787 50.374 1.00 88.73 S ATOM 14317 SG CYS R 83 131.304 57.767 51.579 1.00 79.11 S ATOM 14246 SG CYS R 75 123.323 64.420 41.177 1.00 60.36 S ATOM 14413 SG CYS R 94 126.734 65.574 42.752 1.00 72.62 S ATOM 14110 SG CYS R 53 130.166 54.632 53.835 1.00 97.22 S ATOM 14129 SG CYS R 56 130.119 53.059 57.313 1.00100.77 S ATOM 14196 SG CYS R 68 127.774 51.777 54.409 1.00 92.52 S Time building chain proxies: 9.69, per 1000 atoms: 0.57 Number of scatterers: 16905 At special positions: 0 Unit cell: (145.555, 154.067, 117.466, 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 3 29.99 S 92 16.00 O 3118 8.00 N 2964 7.00 C 10728 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.29 Conformation dependent library (CDL) restraints added in 2.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 80 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 45 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 42 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 83 " pdb=" ZN R 202 " pdb="ZN ZN R 202 " - pdb=" ND1 HIS R 77 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 75 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 94 " pdb=" ZN R 203 " pdb="ZN ZN R 203 " - pdb=" ND1 HIS R 82 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 56 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 68 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 53 " Number of angles added : 6 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4610 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 8 sheets defined 73.1% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'C' and resid 16 through 33 removed outlier: 3.946A pdb=" N ASP C 22 " --> pdb=" O ASP C 18 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ASP C 23 " --> pdb=" O GLN C 19 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA C 26 " --> pdb=" O ASP C 22 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR C 32 " --> pdb=" O ILE C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 55 removed outlier: 3.733A pdb=" N HIS C 48 " --> pdb=" O GLU C 44 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C 49 " --> pdb=" O LEU C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 106 removed outlier: 3.798A pdb=" N LYS C 105 " --> pdb=" O THR C 101 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASP C 106 " --> pdb=" O ASN C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 137 removed outlier: 4.155A pdb=" N LEU C 116 " --> pdb=" O ASP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 143 removed outlier: 3.671A pdb=" N ASN C 141 " --> pdb=" O CYS C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 151 Processing helix chain 'C' and resid 158 through 171 Processing helix chain 'C' and resid 171 through 193 removed outlier: 3.617A pdb=" N LEU C 175 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N LYS C 177 " --> pdb=" O ARG C 173 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N GLN C 178 " --> pdb=" O PRO C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 212 removed outlier: 4.423A pdb=" N ILE C 201 " --> pdb=" O ASN C 197 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY C 212 " --> pdb=" O TYR C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 232 Processing helix chain 'C' and resid 232 through 255 removed outlier: 3.539A pdb=" N GLN C 254 " --> pdb=" O GLU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 279 removed outlier: 3.642A pdb=" N TYR C 260 " --> pdb=" O PRO C 256 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS C 262 " --> pdb=" O THR C 258 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C 279 " --> pdb=" O VAL C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 282 No H-bonds generated for 'chain 'C' and resid 280 through 282' Processing helix chain 'C' and resid 283 through 297 Processing helix chain 'C' and resid 299 through 313 removed outlier: 3.696A pdb=" N GLN C 308 " --> pdb=" O HIS C 304 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN C 309 " --> pdb=" O THR C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 327 Processing helix chain 'C' and resid 333 through 354 Processing helix chain 'C' and resid 355 through 356 No H-bonds generated for 'chain 'C' and resid 355 through 356' Processing helix chain 'C' and resid 357 through 361 Processing helix chain 'C' and resid 362 through 385 removed outlier: 3.577A pdb=" N TYR C 377 " --> pdb=" O VAL C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 405 removed outlier: 3.729A pdb=" N ASN C 404 " --> pdb=" O GLY C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 413 Processing helix chain 'C' and resid 416 through 431 removed outlier: 3.625A pdb=" N GLU C 420 " --> pdb=" O SER C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 454 removed outlier: 3.661A pdb=" N LYS C 454 " --> pdb=" O MET C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 477 removed outlier: 4.111A pdb=" N PHE C 462 " --> pdb=" O ASP C 458 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS C 472 " --> pdb=" O LYS C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 496 removed outlier: 3.541A pdb=" N GLU C 485 " --> pdb=" O SER C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 526 removed outlier: 4.117A pdb=" N MET C 507 " --> pdb=" O LYS C 503 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE C 508 " --> pdb=" O LEU C 504 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR C 526 " --> pdb=" O LYS C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 558 No H-bonds generated for 'chain 'C' and resid 556 through 558' Processing helix chain 'C' and resid 559 through 574 Processing helix chain 'C' and resid 605 through 610 Processing helix chain 'C' and resid 622 through 630 removed outlier: 4.164A pdb=" N ASP C 627 " --> pdb=" O GLN C 623 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER C 628 " --> pdb=" O GLN C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 646 Processing helix chain 'C' and resid 690 through 722 Processing helix chain 'C' and resid 727 through 739 Processing helix chain 'C' and resid 745 through 759 removed outlier: 3.503A pdb=" N ILE C 749 " --> pdb=" O ARG C 745 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 15 Processing helix chain 'D' and resid 19 through 36 Processing helix chain 'D' and resid 43 through 57 removed outlier: 3.694A pdb=" N ARG D 47 " --> pdb=" O ASP D 43 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS D 48 " --> pdb=" O ASP D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 79 removed outlier: 3.699A pdb=" N GLN D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU D 72 " --> pdb=" O ALA D 68 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLY D 73 " --> pdb=" O VAL D 69 " (cutoff:3.500A) Proline residue: D 74 - end of helix removed outlier: 4.036A pdb=" N SER D 77 " --> pdb=" O GLY D 73 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS D 78 " --> pdb=" O PRO D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 96 removed outlier: 3.698A pdb=" N VAL D 84 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR D 86 " --> pdb=" O TYR D 82 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU D 96 " --> pdb=" O CYS D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 116 removed outlier: 3.723A pdb=" N ARG D 103 " --> pdb=" O LYS D 99 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP D 104 " --> pdb=" O GLU D 100 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE D 108 " --> pdb=" O ASP D 104 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY D 109 " --> pdb=" O ILE D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 143 removed outlier: 3.509A pdb=" N LYS D 132 " --> pdb=" O ALA D 128 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG D 137 " --> pdb=" O LYS D 133 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER D 140 " --> pdb=" O GLY D 136 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 143 " --> pdb=" O THR D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 164 removed outlier: 3.968A pdb=" N GLN D 151 " --> pdb=" O ASP D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 184 removed outlier: 3.785A pdb=" N CYS D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) Proline residue: D 182 - end of helix Processing helix chain 'D' and resid 188 through 205 removed outlier: 3.768A pdb=" N ARG D 192 " --> pdb=" O ARG D 188 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE D 197 " --> pdb=" O LYS D 193 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 224 removed outlier: 3.779A pdb=" N PHE D 211 " --> pdb=" O GLY D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 246 Processing helix chain 'D' and resid 247 through 251 removed outlier: 4.194A pdb=" N GLU D 251 " --> pdb=" O ARG D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 264 Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 268 through 286 removed outlier: 3.535A pdb=" N ARG D 272 " --> pdb=" O ASP D 268 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS D 286 " --> pdb=" O PHE D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 292 No H-bonds generated for 'chain 'D' and resid 290 through 292' Processing helix chain 'D' and resid 293 through 306 removed outlier: 4.151A pdb=" N THR D 306 " --> pdb=" O LEU D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 362 removed outlier: 4.008A pdb=" N ARG D 350 " --> pdb=" O SER D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 366 No H-bonds generated for 'chain 'D' and resid 364 through 366' Processing helix chain 'D' and resid 367 through 375 Processing helix chain 'D' and resid 375 through 382 Processing helix chain 'D' and resid 383 through 385 No H-bonds generated for 'chain 'D' and resid 383 through 385' Processing helix chain 'D' and resid 387 through 406 removed outlier: 3.587A pdb=" N ARG D 406 " --> pdb=" O LEU D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 443 Proline residue: D 433 - end of helix removed outlier: 3.668A pdb=" N LYS D 441 " --> pdb=" O LYS D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 465 removed outlier: 3.551A pdb=" N ARG D 451 " --> pdb=" O SER D 447 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS D 454 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE D 455 " --> pdb=" O ARG D 451 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN D 456 " --> pdb=" O GLN D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 485 Proline residue: D 478 - end of helix Processing helix chain 'D' and resid 490 through 507 Processing helix chain 'D' and resid 516 through 529 Proline residue: D 522 - end of helix removed outlier: 3.731A pdb=" N GLY D 529 " --> pdb=" O VAL D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 551 removed outlier: 3.514A pdb=" N THR D 536 " --> pdb=" O PHE D 532 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN D 545 " --> pdb=" O LEU D 541 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG D 551 " --> pdb=" O VAL D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 577 removed outlier: 4.440A pdb=" N ASP D 567 " --> pdb=" O PRO D 563 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N CYS D 571 " --> pdb=" O ASP D 567 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS D 574 " --> pdb=" O THR D 570 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG D 575 " --> pdb=" O CYS D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 601 removed outlier: 3.623A pdb=" N SER D 591 " --> pdb=" O GLU D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 606 through 621 removed outlier: 3.980A pdb=" N ASN D 610 " --> pdb=" O SER D 606 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN D 613 " --> pdb=" O PRO D 609 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE D 614 " --> pdb=" O ASN D 610 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE D 615 " --> pdb=" O THR D 611 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYS D 620 " --> pdb=" O LEU D 616 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASN D 621 " --> pdb=" O GLU D 617 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 637 Processing helix chain 'D' and resid 644 through 658 removed outlier: 4.115A pdb=" N GLY D 649 " --> pdb=" O ARG D 645 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N GLU D 650 " --> pdb=" O PRO D 646 " (cutoff:3.500A) Proline residue: D 653 - end of helix Processing helix chain 'D' and resid 659 through 661 No H-bonds generated for 'chain 'D' and resid 659 through 661' Processing helix chain 'D' and resid 663 through 681 Processing helix chain 'D' and resid 686 through 697 removed outlier: 3.561A pdb=" N ILE D 690 " --> pdb=" O THR D 686 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU D 696 " --> pdb=" O ALA D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 698 through 701 Processing helix chain 'D' and resid 705 through 723 removed outlier: 3.691A pdb=" N SER D 709 " --> pdb=" O ASP D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 730 removed outlier: 4.586A pdb=" N SER D 728 " --> pdb=" O SER D 725 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS D 729 " --> pdb=" O SER D 726 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE D 730 " --> pdb=" O LEU D 727 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 743 removed outlier: 3.604A pdb=" N ASN D 736 " --> pdb=" O GLY D 732 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG D 743 " --> pdb=" O ILE D 739 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 766 removed outlier: 3.668A pdb=" N VAL D 764 " --> pdb=" O GLN D 760 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR D 765 " --> pdb=" O ALA D 761 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY D 766 " --> pdb=" O LEU D 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 771 through 786 Proline residue: D 782 - end of helix Processing helix chain 'D' and resid 793 through 810 removed outlier: 4.174A pdb=" N TYR D 797 " --> pdb=" O LYS D 793 " (cutoff:3.500A) Processing helix chain 'D' and resid 813 through 827 removed outlier: 3.572A pdb=" N VAL D 817 " --> pdb=" O GLU D 813 " (cutoff:3.500A) Processing helix chain 'D' and resid 831 through 847 Processing helix chain 'D' and resid 856 through 864 Processing helix chain 'D' and resid 869 through 887 removed outlier: 3.582A pdb=" N LYS D 873 " --> pdb=" O SER D 869 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN D 887 " --> pdb=" O ILE D 883 " (cutoff:3.500A) Processing helix chain 'D' and resid 887 through 902 Proline residue: D 893 - end of helix removed outlier: 3.977A pdb=" N THR D 900 " --> pdb=" O LEU D 896 " (cutoff:3.500A) Processing helix chain 'D' and resid 906 through 920 Processing helix chain 'D' and resid 921 through 926 Processing helix chain 'D' and resid 928 through 939 removed outlier: 3.601A pdb=" N ILE D 932 " --> pdb=" O TYR D 928 " (cutoff:3.500A) Processing helix chain 'D' and resid 946 through 961 removed outlier: 3.942A pdb=" N VAL D 950 " --> pdb=" O GLY D 946 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL D 951 " --> pdb=" O THR D 947 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU D 960 " --> pdb=" O GLY D 956 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE D 961 " --> pdb=" O LYS D 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 962 through 973 removed outlier: 3.512A pdb=" N LEU D 966 " --> pdb=" O ASP D 962 " (cutoff:3.500A) Proline residue: D 968 - end of helix removed outlier: 3.852A pdb=" N TYR D 973 " --> pdb=" O ARG D 969 " (cutoff:3.500A) Processing helix chain 'D' and resid 978 through 990 removed outlier: 3.829A pdb=" N ARG D 982 " --> pdb=" O SER D 978 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER D 983 " --> pdb=" O SER D 979 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS D 990 " --> pdb=" O VAL D 986 " (cutoff:3.500A) Processing helix chain 'D' and resid 991 through 993 No H-bonds generated for 'chain 'D' and resid 991 through 993' Processing helix chain 'D' and resid 1000 through 1013 removed outlier: 3.740A pdb=" N LYS D1005 " --> pdb=" O ASP D1001 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASN D1006 " --> pdb=" O PRO D1002 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N CYS D1007 " --> pdb=" O LEU D1003 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N GLY D1009 " --> pdb=" O LYS D1005 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ASP D1010 " --> pdb=" O ASN D1006 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N PHE D1011 " --> pdb=" O CYS D1007 " (cutoff:3.500A) Processing helix chain 'D' and resid 1019 through 1037 removed outlier: 3.845A pdb=" N ARG D1023 " --> pdb=" O ASP D1019 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG D1024 " --> pdb=" O LEU D1020 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL D1025 " --> pdb=" O ASN D1021 " (cutoff:3.500A) Processing helix chain 'D' and resid 1038 through 1041 Processing helix chain 'D' and resid 1042 through 1043 No H-bonds generated for 'chain 'D' and resid 1042 through 1043' Processing helix chain 'D' and resid 1044 through 1057 Proline residue: D1050 - end of helix removed outlier: 3.513A pdb=" N ASN D1054 " --> pdb=" O PRO D1050 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU D1055 " --> pdb=" O HIS D1051 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR D1056 " --> pdb=" O LEU D1052 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS D1057 " --> pdb=" O TYR D1053 " (cutoff:3.500A) Processing helix chain 'D' and resid 1059 through 1063 Processing helix chain 'D' and resid 1078 through 1096 removed outlier: 3.653A pdb=" N ARG D1082 " --> pdb=" O GLY D1078 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER D1095 " --> pdb=" O THR D1091 " (cutoff:3.500A) Processing helix chain 'D' and resid 1101 through 1114 removed outlier: 3.795A pdb=" N LYS D1114 " --> pdb=" O GLU D1110 " (cutoff:3.500A) Processing helix chain 'D' and resid 1116 through 1133 removed outlier: 3.911A pdb=" N THR D1132 " --> pdb=" O VAL D1128 " (cutoff:3.500A) Processing helix chain 'D' and resid 1134 through 1139 removed outlier: 4.247A pdb=" N VAL D1138 " --> pdb=" O CYS D1134 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU D1139 " --> pdb=" O PRO D1135 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1134 through 1139' Processing helix chain 'D' and resid 1141 through 1154 removed outlier: 4.051A pdb=" N GLU D1147 " --> pdb=" O ASP D1143 " (cutoff:3.500A) Proline residue: D1148 - end of helix Processing helix chain 'D' and resid 1162 through 1185 removed outlier: 3.564A pdb=" N PHE D1166 " --> pdb=" O VAL D1162 " (cutoff:3.500A) Processing helix chain 'D' and resid 1192 through 1205 removed outlier: 3.647A pdb=" N GLU D1197 " --> pdb=" O PRO D1193 " (cutoff:3.500A) Processing helix chain 'D' and resid 1205 through 1216 Processing helix chain 'R' and resid 53 through 59 Processing helix chain 'R' and resid 62 through 67 removed outlier: 3.533A pdb=" N GLU R 66 " --> pdb=" O SER R 62 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU R 67 " --> pdb=" O ALA R 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 62 through 67' Processing helix chain 'R' and resid 81 through 88 Processing helix chain 'S' and resid 17 through 22 Processing helix chain 'S' and resid 24 through 34 removed outlier: 3.574A pdb=" N ASP S 33 " --> pdb=" O THR S 29 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU S 34 " --> pdb=" O MET S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 51 through 65 removed outlier: 3.570A pdb=" N LEU S 55 " --> pdb=" O ASN S 51 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYS S 56 " --> pdb=" O ALA S 52 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS S 57 " --> pdb=" O ALA S 53 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 94 Processing helix chain 'S' and resid 96 through 110 Processing helix chain 'S' and resid 112 through 128 Processing helix chain 'S' and resid 131 through 140 removed outlier: 3.526A pdb=" N ARG S 136 " --> pdb=" O PRO S 132 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS S 137 " --> pdb=" O GLU S 133 " (cutoff:3.500A) Processing helix chain 'S' and resid 146 through 159 removed outlier: 3.500A pdb=" N GLU S 156 " --> pdb=" O GLN S 152 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN S 158 " --> pdb=" O ARG S 154 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N TRP S 159 " --> pdb=" O LYS S 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 109 removed outlier: 3.515A pdb=" N LEU F 105 " --> pdb=" O PRO F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 112 No H-bonds generated for 'chain 'F' and resid 110 through 112' Processing helix chain 'F' and resid 113 through 122 removed outlier: 4.175A pdb=" N GLY F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 132 removed outlier: 3.665A pdb=" N TYR F 128 " --> pdb=" O CYS F 124 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ARG F 129 " --> pdb=" O LYS F 125 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU F 130 " --> pdb=" O ARG F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 137 No H-bonds generated for 'chain 'F' and resid 135 through 137' Processing helix chain 'F' and resid 148 through 158 Processing helix chain 'F' and resid 194 through 203 Processing helix chain 'F' and resid 219 through 227 Processing helix chain 'F' and resid 244 through 255 Processing helix chain 'F' and resid 270 through 280 Processing helix chain 'F' and resid 298 through 309 Processing helix chain 'F' and resid 324 through 334 removed outlier: 3.734A pdb=" N LEU F 334 " --> pdb=" O GLU F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 359 Processing helix chain 'F' and resid 374 through 383 removed outlier: 3.973A pdb=" N LEU F 378 " --> pdb=" O GLY F 374 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 534 through 541 removed outlier: 5.157A pdb=" N VAL R 24 " --> pdb=" O VAL C 591 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL C 591 " --> pdb=" O VAL R 24 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS R 26 " --> pdb=" O GLU C 589 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N VAL R 30 " --> pdb=" O LEU C 585 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU C 585 " --> pdb=" O VAL R 30 " (cutoff:3.500A) removed outlier: 11.878A pdb=" N LEU R 32 " --> pdb=" O TYR C 583 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N TYR C 583 " --> pdb=" O LEU R 32 " (cutoff:3.500A) removed outlier: 10.889A pdb=" N ALA R 34 " --> pdb=" O TRP C 581 " (cutoff:3.500A) removed outlier: 10.484A pdb=" N TRP C 581 " --> pdb=" O ALA R 34 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL C 682 " --> pdb=" O THR C 600 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 619 through 621 Processing sheet with id=AA3, first strand: chain 'C' and resid 724 through 726 Processing sheet with id=AA4, first strand: chain 'R' and resid 79 through 80 removed outlier: 4.275A pdb=" N LYS R 105 " --> pdb=" O TRP R 72 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'S' and resid 14 through 16 removed outlier: 3.923A pdb=" N LEU S 6 " --> pdb=" O PHE S 14 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL S 16 " --> pdb=" O ILE S 4 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 139 through 141 removed outlier: 7.235A pdb=" N LEU F 140 " --> pdb=" O ARG F 164 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 260 through 262 Processing sheet with id=AA8, first strand: chain 'F' and resid 339 through 341 1094 hydrogen bonds defined for protein. 3219 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: 5.34 Time building geometry restraints manager: 4.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5022 1.34 - 1.46: 2334 1.46 - 1.58: 9681 1.58 - 1.70: 0 1.70 - 1.82: 131 Bond restraints: 17168 Sorted by residual: bond pdb=" C LEU F 114 " pdb=" N PRO F 115 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.20e-02 6.94e+03 3.21e+00 bond pdb=" CA CYS D1134 " pdb=" CB CYS D1134 " ideal model delta sigma weight residual 1.525 1.536 -0.011 8.30e-03 1.45e+04 1.90e+00 bond pdb=" N ASN D 662 " pdb=" CA ASN D 662 " ideal model delta sigma weight residual 1.457 1.474 -0.016 1.29e-02 6.01e+03 1.56e+00 bond pdb=" CG LEU D1015 " pdb=" CD1 LEU D1015 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.15e+00 bond pdb=" C THR D 780 " pdb=" N GLY D 781 " ideal model delta sigma weight residual 1.330 1.346 -0.016 1.49e-02 4.50e+03 1.12e+00 ... (remaining 17163 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 23149 2.03 - 4.07: 242 4.07 - 6.10: 41 6.10 - 8.14: 6 8.14 - 10.17: 2 Bond angle restraints: 23440 Sorted by residual: angle pdb=" C VAL C 277 " pdb=" N TYR C 278 " pdb=" CA TYR C 278 " ideal model delta sigma weight residual 122.50 116.27 6.23 1.82e+00 3.02e-01 1.17e+01 angle pdb=" N ASN D 769 " pdb=" CA ASN D 769 " pdb=" C ASN D 769 " ideal model delta sigma weight residual 113.23 109.45 3.78 1.22e+00 6.72e-01 9.62e+00 angle pdb=" N ILE D1000 " pdb=" CA ILE D1000 " pdb=" C ILE D1000 " ideal model delta sigma weight residual 113.07 108.87 4.20 1.36e+00 5.41e-01 9.54e+00 angle pdb=" N ASP C 109 " pdb=" CA ASP C 109 " pdb=" C ASP C 109 " ideal model delta sigma weight residual 112.24 108.30 3.94 1.28e+00 6.10e-01 9.46e+00 angle pdb=" CA LEU F 114 " pdb=" CB LEU F 114 " pdb=" CG LEU F 114 " ideal model delta sigma weight residual 116.30 126.47 -10.17 3.50e+00 8.16e-02 8.44e+00 ... (remaining 23435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.18: 9536 15.18 - 30.37: 636 30.37 - 45.55: 135 45.55 - 60.74: 29 60.74 - 75.92: 19 Dihedral angle restraints: 10355 sinusoidal: 3307 harmonic: 7048 Sorted by residual: dihedral pdb=" CA LEU R 96 " pdb=" C LEU R 96 " pdb=" N ASP R 97 " pdb=" CA ASP R 97 " ideal model delta harmonic sigma weight residual -180.00 -154.60 -25.40 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA PHE C 232 " pdb=" C PHE C 232 " pdb=" N GLU C 233 " pdb=" CA GLU C 233 " ideal model delta harmonic sigma weight residual -180.00 -164.07 -15.93 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CG ARG D1178 " pdb=" CD ARG D1178 " pdb=" NE ARG D1178 " pdb=" CZ ARG D1178 " ideal model delta sinusoidal sigma weight residual 90.00 132.81 -42.81 2 1.50e+01 4.44e-03 9.85e+00 ... (remaining 10352 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1837 0.029 - 0.059: 726 0.059 - 0.088: 231 0.088 - 0.118: 102 0.118 - 0.147: 13 Chirality restraints: 2909 Sorted by residual: chirality pdb=" CB VAL D 290 " pdb=" CA VAL D 290 " pdb=" CG1 VAL D 290 " pdb=" CG2 VAL D 290 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CA THR D 374 " pdb=" N THR D 374 " pdb=" C THR D 374 " pdb=" CB THR D 374 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.27e-01 chirality pdb=" CA ASN D 662 " pdb=" N ASN D 662 " pdb=" C ASN D 662 " pdb=" CB ASN D 662 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.77e-01 ... (remaining 2906 not shown) Planarity restraints: 2996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 181 " -0.050 5.00e-02 4.00e+02 7.51e-02 9.02e+00 pdb=" N PRO D 182 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO D 182 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 182 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP C 545 " 0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO C 546 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO C 546 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 546 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 814 " -0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO D 815 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO D 815 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 815 " -0.023 5.00e-02 4.00e+02 ... (remaining 2993 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 60 2.58 - 3.16: 14051 3.16 - 3.74: 25518 3.74 - 4.32: 31760 4.32 - 4.90: 55165 Nonbonded interactions: 126554 Sorted by model distance: nonbonded pdb=" OD2 ASP R 97 " pdb="ZN ZN R 202 " model vdw 2.006 2.230 nonbonded pdb=" OE1 GLU C 190 " pdb=" OH TYR C 278 " model vdw 2.178 3.040 nonbonded pdb=" O GLU D1165 " pdb=" NE2 GLN D1169 " model vdw 2.197 3.120 nonbonded pdb=" OH TYR C 244 " pdb=" OE2 GLU C 271 " model vdw 2.215 3.040 nonbonded pdb=" NZ LYS D 971 " pdb=" OD2 ASP D1010 " model vdw 2.233 3.120 ... (remaining 126549 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 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: 0.020 Extract box with map and model: 0.680 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 40.770 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.060 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 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 0.268 17179 Z= 0.147 Angle : 0.571 10.169 23446 Z= 0.318 Chirality : 0.038 0.147 2909 Planarity : 0.004 0.075 2996 Dihedral : 11.832 75.924 5745 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: 1.31 (0.18), residues: 2358 helix: 1.92 (0.13), residues: 1543 sheet: -3.12 (0.58), residues: 57 loop : -1.02 (0.21), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 545 HIS 0.005 0.001 HIS D 173 PHE 0.017 0.001 PHE C 402 TYR 0.017 0.001 TYR D1117 ARG 0.008 0.000 ARG D1042 Details of bonding type rmsd hydrogen bonds : bond 0.18466 ( 1094) hydrogen bonds : angle 4.89365 ( 3219) metal coordination : bond 0.08336 ( 11) metal coordination : angle 4.68766 ( 6) covalent geometry : bond 0.00262 (17168) covalent geometry : angle 0.56579 (23440) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 385 time to evaluate : 2.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 48 HIS cc_start: 0.8206 (m90) cc_final: 0.6825 (m90) REVERT: C 97 LYS cc_start: 0.8499 (ttmm) cc_final: 0.8259 (ttmm) REVERT: C 117 LYS cc_start: 0.7695 (mtpp) cc_final: 0.7411 (mtpp) REVERT: C 124 GLU cc_start: 0.6946 (tp30) cc_final: 0.6705 (mm-30) REVERT: C 131 LYS cc_start: 0.7913 (tppp) cc_final: 0.7707 (tppp) REVERT: C 170 CYS cc_start: 0.7107 (m) cc_final: 0.6853 (m) REVERT: C 241 GLU cc_start: 0.6858 (mt-10) cc_final: 0.6650 (mt-10) REVERT: C 372 ASP cc_start: 0.6969 (m-30) cc_final: 0.6745 (m-30) REVERT: C 478 ASN cc_start: 0.7984 (p0) cc_final: 0.7680 (p0) REVERT: C 493 LYS cc_start: 0.8250 (mttt) cc_final: 0.8031 (mttm) REVERT: C 697 GLU cc_start: 0.6773 (mt-10) cc_final: 0.6481 (mt-10) REVERT: C 755 ILE cc_start: 0.8349 (tp) cc_final: 0.8129 (tp) REVERT: D 8 ILE cc_start: 0.8321 (mm) cc_final: 0.7997 (mt) REVERT: D 12 LEU cc_start: 0.8419 (mt) cc_final: 0.8037 (mp) REVERT: D 34 LEU cc_start: 0.8326 (mm) cc_final: 0.8060 (mp) REVERT: D 70 LYS cc_start: 0.7804 (mttp) cc_final: 0.7435 (mttp) REVERT: D 78 LYS cc_start: 0.7940 (mmmm) cc_final: 0.7598 (mmmm) REVERT: D 186 SER cc_start: 0.8612 (m) cc_final: 0.8391 (m) REVERT: D 489 SER cc_start: 0.8288 (m) cc_final: 0.8067 (m) REVERT: D 496 ASP cc_start: 0.6987 (m-30) cc_final: 0.6640 (m-30) REVERT: D 647 VAL cc_start: 0.8319 (t) cc_final: 0.8020 (p) REVERT: D 769 ASN cc_start: 0.6922 (t0) cc_final: 0.6578 (t0) REVERT: D 849 ILE cc_start: 0.8562 (mm) cc_final: 0.8353 (mt) REVERT: D 882 SER cc_start: 0.8414 (m) cc_final: 0.7830 (t) REVERT: D 1140 GLN cc_start: 0.8214 (pm20) cc_final: 0.7905 (pm20) outliers start: 0 outliers final: 0 residues processed: 385 average time/residue: 0.3068 time to fit residues: 172.5207 Evaluate side-chains 347 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 200 optimal weight: 0.4980 chunk 179 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 121 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 185 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 215 optimal weight: 30.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 ASN C 737 GLN D 101 GLN D 404 GLN D 931 ASN D1169 GLN R 76 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.130886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.103749 restraints weight = 26256.457| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.79 r_work: 0.3118 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17179 Z= 0.136 Angle : 0.531 8.275 23446 Z= 0.277 Chirality : 0.040 0.171 2909 Planarity : 0.004 0.058 2996 Dihedral : 3.576 16.040 2515 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.22 % Allowed : 6.57 % Favored : 92.21 % 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: 1.65 (0.18), residues: 2358 helix: 2.19 (0.13), residues: 1552 sheet: -2.76 (0.62), residues: 65 loop : -0.94 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP S 61 HIS 0.004 0.001 HIS D 173 PHE 0.024 0.001 PHE C 402 TYR 0.016 0.002 TYR C 377 ARG 0.005 0.000 ARG D1042 Details of bonding type rmsd hydrogen bonds : bond 0.05076 ( 1094) hydrogen bonds : angle 3.86521 ( 3219) metal coordination : bond 0.00557 ( 11) metal coordination : angle 1.13576 ( 6) covalent geometry : bond 0.00299 (17168) covalent geometry : angle 0.53059 (23440) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 360 time to evaluate : 1.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 30 GLN cc_start: 0.8629 (tt0) cc_final: 0.8411 (tt0) REVERT: C 44 GLU cc_start: 0.8127 (tp30) cc_final: 0.7904 (tp30) REVERT: C 97 LYS cc_start: 0.8943 (ttmm) cc_final: 0.8623 (ttmm) REVERT: C 124 GLU cc_start: 0.7858 (tp30) cc_final: 0.7622 (mm-30) REVERT: C 131 LYS cc_start: 0.8472 (tppp) cc_final: 0.8256 (tppp) REVERT: C 170 CYS cc_start: 0.8105 (m) cc_final: 0.7888 (m) REVERT: C 199 ARG cc_start: 0.8446 (tpp80) cc_final: 0.8233 (ttm110) REVERT: C 259 GLU cc_start: 0.7387 (mp0) cc_final: 0.7170 (mt-10) REVERT: C 372 ASP cc_start: 0.7936 (m-30) cc_final: 0.7704 (m-30) REVERT: C 478 ASN cc_start: 0.8163 (p0) cc_final: 0.7789 (p0) REVERT: C 509 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.8177 (mt0) REVERT: C 694 GLN cc_start: 0.7827 (mm-40) cc_final: 0.7617 (mm-40) REVERT: C 697 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7409 (mt-10) REVERT: D 35 GLN cc_start: 0.7699 (mt0) cc_final: 0.7451 (mt0) REVERT: D 70 LYS cc_start: 0.8201 (mttp) cc_final: 0.7922 (mttp) REVERT: D 78 LYS cc_start: 0.8242 (mmmm) cc_final: 0.8021 (mmmm) REVERT: D 177 LEU cc_start: 0.8421 (tt) cc_final: 0.8218 (tt) REVERT: D 457 MET cc_start: 0.8391 (tpp) cc_final: 0.7901 (tpp) REVERT: D 496 ASP cc_start: 0.7705 (m-30) cc_final: 0.7394 (m-30) REVERT: D 769 ASN cc_start: 0.7663 (t0) cc_final: 0.7308 (t0) REVERT: D 1195 MET cc_start: 0.7519 (tpp) cc_final: 0.7253 (tpp) outliers start: 19 outliers final: 8 residues processed: 368 average time/residue: 0.3139 time to fit residues: 167.1400 Evaluate side-chains 347 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 338 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 509 GLN Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 586 SER Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 1004 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 203 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 164 optimal weight: 0.5980 chunk 163 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 230 optimal weight: 9.9990 chunk 105 optimal weight: 0.9980 chunk 132 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 141 ASN C 143 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.130995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.103883 restraints weight = 26486.706| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.88 r_work: 0.3110 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17179 Z= 0.124 Angle : 0.494 7.889 23446 Z= 0.257 Chirality : 0.039 0.296 2909 Planarity : 0.004 0.048 2996 Dihedral : 3.464 15.679 2515 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.74 % Allowed : 9.47 % Favored : 88.80 % 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: 1.82 (0.18), residues: 2358 helix: 2.31 (0.13), residues: 1562 sheet: -2.59 (0.64), residues: 65 loop : -0.92 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP S 61 HIS 0.004 0.001 HIS D 173 PHE 0.023 0.001 PHE C 402 TYR 0.015 0.001 TYR C 377 ARG 0.009 0.000 ARG D1059 Details of bonding type rmsd hydrogen bonds : bond 0.04626 ( 1094) hydrogen bonds : angle 3.66784 ( 3219) metal coordination : bond 0.00435 ( 11) metal coordination : angle 1.04753 ( 6) covalent geometry : bond 0.00277 (17168) covalent geometry : angle 0.49352 (23440) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 348 time to evaluate : 1.827 Fit side-chains revert: symmetry clash REVERT: C 30 GLN cc_start: 0.8654 (tt0) cc_final: 0.8451 (tt0) REVERT: C 44 GLU cc_start: 0.8103 (tp30) cc_final: 0.7729 (tp30) REVERT: C 97 LYS cc_start: 0.8905 (ttmm) cc_final: 0.8641 (ttmm) REVERT: C 124 GLU cc_start: 0.7947 (tp30) cc_final: 0.7661 (mm-30) REVERT: C 131 LYS cc_start: 0.8469 (tppp) cc_final: 0.8225 (tppp) REVERT: C 170 CYS cc_start: 0.8135 (m) cc_final: 0.7901 (m) REVERT: C 259 GLU cc_start: 0.7373 (mp0) cc_final: 0.7142 (mt-10) REVERT: C 372 ASP cc_start: 0.7983 (m-30) cc_final: 0.7781 (m-30) REVERT: C 478 ASN cc_start: 0.8226 (p0) cc_final: 0.7850 (p0) REVERT: C 509 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.8150 (mt0) REVERT: C 641 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8044 (mp10) REVERT: C 697 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7449 (mt-10) REVERT: D 35 GLN cc_start: 0.7694 (mt0) cc_final: 0.7450 (mt0) REVERT: D 78 LYS cc_start: 0.8256 (mmmm) cc_final: 0.8044 (mmmm) REVERT: D 177 LEU cc_start: 0.8389 (tt) cc_final: 0.8164 (tt) REVERT: D 185 THR cc_start: 0.8848 (p) cc_final: 0.8495 (t) REVERT: D 457 MET cc_start: 0.8438 (tpp) cc_final: 0.7993 (tpp) REVERT: D 481 ILE cc_start: 0.8577 (mm) cc_final: 0.8333 (mm) REVERT: D 496 ASP cc_start: 0.7767 (m-30) cc_final: 0.7425 (m-30) REVERT: D 769 ASN cc_start: 0.7646 (t0) cc_final: 0.7169 (t0) REVERT: D 973 TYR cc_start: 0.8560 (m-80) cc_final: 0.8314 (m-80) REVERT: D 1059 ARG cc_start: 0.7399 (ttp80) cc_final: 0.7153 (ttp80) REVERT: D 1099 ARG cc_start: 0.8381 (mmm-85) cc_final: 0.8109 (mmt180) REVERT: D 1195 MET cc_start: 0.7533 (tpp) cc_final: 0.7191 (tpp) outliers start: 27 outliers final: 12 residues processed: 356 average time/residue: 0.3109 time to fit residues: 160.3379 Evaluate side-chains 345 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 331 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 509 GLN Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 586 SER Chi-restraints excluded: chain C residue 641 GLN Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 689 MET Chi-restraints excluded: chain D residue 768 ASN Chi-restraints excluded: chain D residue 901 SER Chi-restraints excluded: chain D residue 922 VAL Chi-restraints excluded: chain D residue 967 LEU Chi-restraints excluded: chain F residue 96 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 43 optimal weight: 0.9980 chunk 62 optimal weight: 7.9990 chunk 158 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 200 optimal weight: 0.6980 chunk 169 optimal weight: 4.9990 chunk 174 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 216 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 141 ASN C 494 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.130169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.103090 restraints weight = 26471.020| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.87 r_work: 0.3097 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17179 Z= 0.137 Angle : 0.494 7.511 23446 Z= 0.256 Chirality : 0.040 0.264 2909 Planarity : 0.004 0.045 2996 Dihedral : 3.441 15.839 2515 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.61 % Allowed : 11.08 % Favored : 87.31 % 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: 1.87 (0.18), residues: 2358 helix: 2.33 (0.13), residues: 1571 sheet: -2.63 (0.63), residues: 65 loop : -0.89 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP S 61 HIS 0.004 0.001 HIS D 707 PHE 0.024 0.001 PHE C 402 TYR 0.017 0.002 TYR C 32 ARG 0.007 0.000 ARG C 741 Details of bonding type rmsd hydrogen bonds : bond 0.04760 ( 1094) hydrogen bonds : angle 3.60216 ( 3219) metal coordination : bond 0.00532 ( 11) metal coordination : angle 1.11124 ( 6) covalent geometry : bond 0.00315 (17168) covalent geometry : angle 0.49345 (23440) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 349 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 30 GLN cc_start: 0.8638 (tt0) cc_final: 0.8429 (tt0) REVERT: C 44 GLU cc_start: 0.8118 (tp30) cc_final: 0.7652 (tp30) REVERT: C 97 LYS cc_start: 0.8917 (ttmm) cc_final: 0.8661 (ttmm) REVERT: C 124 GLU cc_start: 0.7956 (tp30) cc_final: 0.7661 (mm-30) REVERT: C 131 LYS cc_start: 0.8530 (tppp) cc_final: 0.8261 (tppp) REVERT: C 170 CYS cc_start: 0.8168 (m) cc_final: 0.7910 (m) REVERT: C 259 GLU cc_start: 0.7459 (mp0) cc_final: 0.7215 (mt-10) REVERT: C 478 ASN cc_start: 0.8258 (p0) cc_final: 0.7853 (p0) REVERT: C 509 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8141 (mt0) REVERT: C 641 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8032 (mp10) REVERT: C 697 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7491 (mt-10) REVERT: D 35 GLN cc_start: 0.7665 (mt0) cc_final: 0.7425 (mt0) REVERT: D 78 LYS cc_start: 0.8280 (mmmm) cc_final: 0.8044 (mmmm) REVERT: D 177 LEU cc_start: 0.8408 (tt) cc_final: 0.8176 (tt) REVERT: D 185 THR cc_start: 0.8829 (p) cc_final: 0.8500 (t) REVERT: D 399 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8254 (mm) REVERT: D 457 MET cc_start: 0.8405 (tpp) cc_final: 0.7902 (tpp) REVERT: D 496 ASP cc_start: 0.7781 (m-30) cc_final: 0.7441 (m-30) REVERT: D 737 GLU cc_start: 0.8241 (mm-30) cc_final: 0.8016 (mm-30) REVERT: D 769 ASN cc_start: 0.7664 (t0) cc_final: 0.7258 (t0) REVERT: D 857 LEU cc_start: 0.8723 (tp) cc_final: 0.8369 (tt) REVERT: D 1099 ARG cc_start: 0.8408 (mmm-85) cc_final: 0.8142 (mmt180) outliers start: 25 outliers final: 12 residues processed: 358 average time/residue: 0.3074 time to fit residues: 160.8349 Evaluate side-chains 356 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 341 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 509 GLN Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 586 SER Chi-restraints excluded: chain C residue 641 GLN Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 689 MET Chi-restraints excluded: chain D residue 901 SER Chi-restraints excluded: chain D residue 922 VAL Chi-restraints excluded: chain D residue 967 LEU Chi-restraints excluded: chain D residue 1127 LEU Chi-restraints excluded: chain D residue 1142 LEU Chi-restraints excluded: chain F residue 96 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 137 optimal weight: 0.9980 chunk 152 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 146 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 189 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 141 ASN D1021 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.130060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.102749 restraints weight = 26733.990| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.88 r_work: 0.3091 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17179 Z= 0.133 Angle : 0.488 7.726 23446 Z= 0.253 Chirality : 0.039 0.193 2909 Planarity : 0.004 0.046 2996 Dihedral : 3.433 16.344 2515 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.61 % Allowed : 12.88 % Favored : 85.51 % 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: 1.91 (0.18), residues: 2358 helix: 2.35 (0.13), residues: 1573 sheet: -2.68 (0.62), residues: 65 loop : -0.85 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 144 HIS 0.004 0.001 HIS D 707 PHE 0.022 0.001 PHE C 402 TYR 0.020 0.002 TYR D 878 ARG 0.008 0.000 ARG D1059 Details of bonding type rmsd hydrogen bonds : bond 0.04634 ( 1094) hydrogen bonds : angle 3.54003 ( 3219) metal coordination : bond 0.00473 ( 11) metal coordination : angle 1.11871 ( 6) covalent geometry : bond 0.00307 (17168) covalent geometry : angle 0.48730 (23440) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 355 time to evaluate : 2.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 30 GLN cc_start: 0.8636 (tt0) cc_final: 0.8424 (tt0) REVERT: C 44 GLU cc_start: 0.8086 (tp30) cc_final: 0.7649 (tp30) REVERT: C 97 LYS cc_start: 0.8909 (ttmm) cc_final: 0.8657 (ttmm) REVERT: C 124 GLU cc_start: 0.7956 (tp30) cc_final: 0.7658 (mm-30) REVERT: C 131 LYS cc_start: 0.8552 (tppp) cc_final: 0.8266 (tppp) REVERT: C 170 CYS cc_start: 0.8131 (m) cc_final: 0.7909 (m) REVERT: C 259 GLU cc_start: 0.7487 (mp0) cc_final: 0.7154 (mp0) REVERT: C 478 ASN cc_start: 0.8263 (p0) cc_final: 0.7862 (p0) REVERT: C 509 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8153 (mt0) REVERT: C 563 TYR cc_start: 0.8115 (t80) cc_final: 0.7865 (t80) REVERT: C 641 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.8014 (mp10) REVERT: C 697 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7503 (mt-10) REVERT: D 177 LEU cc_start: 0.8408 (tt) cc_final: 0.8195 (tt) REVERT: D 185 THR cc_start: 0.8815 (p) cc_final: 0.8505 (t) REVERT: D 399 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8231 (mm) REVERT: D 457 MET cc_start: 0.8373 (tpp) cc_final: 0.7862 (tpp) REVERT: D 485 ASN cc_start: 0.7868 (p0) cc_final: 0.7592 (p0) REVERT: D 496 ASP cc_start: 0.7791 (m-30) cc_final: 0.7434 (m-30) REVERT: D 538 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7936 (tp30) REVERT: D 689 MET cc_start: 0.7015 (OUTLIER) cc_final: 0.6747 (ptp) REVERT: D 737 GLU cc_start: 0.8244 (mm-30) cc_final: 0.8040 (mm-30) REVERT: D 769 ASN cc_start: 0.7682 (t0) cc_final: 0.7257 (t0) REVERT: D 857 LEU cc_start: 0.8696 (tp) cc_final: 0.8354 (tt) REVERT: D 1059 ARG cc_start: 0.7554 (ttp80) cc_final: 0.7226 (ttp80) REVERT: D 1099 ARG cc_start: 0.8435 (mmm-85) cc_final: 0.8165 (mmt180) REVERT: D 1195 MET cc_start: 0.7533 (tpp) cc_final: 0.7241 (tpp) outliers start: 25 outliers final: 15 residues processed: 364 average time/residue: 0.3033 time to fit residues: 160.4880 Evaluate side-chains 362 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 343 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain C residue 509 GLN Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 586 SER Chi-restraints excluded: chain C residue 641 GLN Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 689 MET Chi-restraints excluded: chain D residue 849 ILE Chi-restraints excluded: chain D residue 901 SER Chi-restraints excluded: chain D residue 922 VAL Chi-restraints excluded: chain D residue 967 LEU Chi-restraints excluded: chain D residue 1127 LEU Chi-restraints excluded: chain D residue 1142 LEU Chi-restraints excluded: chain D residue 1184 LEU Chi-restraints excluded: chain F residue 96 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 172 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 206 optimal weight: 0.9990 chunk 207 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 141 ASN C 494 GLN ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.129293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.101986 restraints weight = 26432.486| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.85 r_work: 0.3090 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17179 Z= 0.140 Angle : 0.494 8.202 23446 Z= 0.256 Chirality : 0.039 0.235 2909 Planarity : 0.004 0.047 2996 Dihedral : 3.429 16.478 2515 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.25 % Allowed : 13.78 % Favored : 83.97 % 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: 1.91 (0.18), residues: 2358 helix: 2.35 (0.13), residues: 1572 sheet: -2.70 (0.61), residues: 65 loop : -0.84 (0.22), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 144 HIS 0.005 0.001 HIS D 707 PHE 0.023 0.001 PHE C 402 TYR 0.017 0.002 TYR C 278 ARG 0.007 0.000 ARG C 242 Details of bonding type rmsd hydrogen bonds : bond 0.04741 ( 1094) hydrogen bonds : angle 3.53490 ( 3219) metal coordination : bond 0.00530 ( 11) metal coordination : angle 1.14930 ( 6) covalent geometry : bond 0.00328 (17168) covalent geometry : angle 0.49367 (23440) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 354 time to evaluate : 1.796 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 30 GLN cc_start: 0.8634 (tt0) cc_final: 0.8413 (tt0) REVERT: C 44 GLU cc_start: 0.8102 (tp30) cc_final: 0.7694 (tp30) REVERT: C 97 LYS cc_start: 0.8915 (ttmm) cc_final: 0.8672 (ttmm) REVERT: C 124 GLU cc_start: 0.7959 (tp30) cc_final: 0.7654 (mm-30) REVERT: C 131 LYS cc_start: 0.8570 (tppp) cc_final: 0.8271 (tppp) REVERT: C 146 ARG cc_start: 0.7716 (mtm110) cc_final: 0.7473 (mtm110) REVERT: C 170 CYS cc_start: 0.8167 (m) cc_final: 0.7922 (m) REVERT: C 199 ARG cc_start: 0.8484 (mtp180) cc_final: 0.8262 (mmm-85) REVERT: C 259 GLU cc_start: 0.7563 (mp0) cc_final: 0.7208 (mp0) REVERT: C 478 ASN cc_start: 0.8265 (p0) cc_final: 0.7859 (p0) REVERT: C 509 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.8118 (mt0) REVERT: C 641 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.8015 (mp10) REVERT: C 697 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7515 (mt-10) REVERT: D 177 LEU cc_start: 0.8417 (tt) cc_final: 0.8210 (tt) REVERT: D 185 THR cc_start: 0.8833 (p) cc_final: 0.8501 (t) REVERT: D 290 VAL cc_start: 0.8151 (m) cc_final: 0.7907 (p) REVERT: D 457 MET cc_start: 0.8354 (tpp) cc_final: 0.7913 (tpp) REVERT: D 485 ASN cc_start: 0.7844 (p0) cc_final: 0.7574 (p0) REVERT: D 496 ASP cc_start: 0.7791 (m-30) cc_final: 0.7438 (m-30) REVERT: D 689 MET cc_start: 0.7041 (OUTLIER) cc_final: 0.6781 (ptp) REVERT: D 769 ASN cc_start: 0.7722 (t0) cc_final: 0.7288 (t0) REVERT: D 857 LEU cc_start: 0.8694 (tp) cc_final: 0.8361 (tt) REVERT: D 1059 ARG cc_start: 0.7531 (ttp80) cc_final: 0.7330 (ttp80) REVERT: D 1083 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8154 (mtpt) REVERT: D 1099 ARG cc_start: 0.8441 (mmm-85) cc_final: 0.8163 (mmt180) outliers start: 35 outliers final: 22 residues processed: 369 average time/residue: 0.3275 time to fit residues: 177.4959 Evaluate side-chains 372 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 346 time to evaluate : 1.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 509 GLN Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 536 SER Chi-restraints excluded: chain C residue 586 SER Chi-restraints excluded: chain C residue 641 GLN Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain D residue 689 MET Chi-restraints excluded: chain D residue 849 ILE Chi-restraints excluded: chain D residue 901 SER Chi-restraints excluded: chain D residue 922 VAL Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 967 LEU Chi-restraints excluded: chain D residue 1012 LEU Chi-restraints excluded: chain D residue 1022 VAL Chi-restraints excluded: chain D residue 1083 LYS Chi-restraints excluded: chain D residue 1127 LEU Chi-restraints excluded: chain D residue 1142 LEU Chi-restraints excluded: chain D residue 1184 LEU Chi-restraints excluded: chain F residue 96 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 46 optimal weight: 0.9980 chunk 41 optimal weight: 0.4980 chunk 167 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 115 optimal weight: 0.0770 chunk 61 optimal weight: 0.0020 chunk 139 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 119 optimal weight: 0.0670 overall best weight: 0.2884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.131546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.104051 restraints weight = 26468.874| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.86 r_work: 0.3119 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 17179 Z= 0.098 Angle : 0.477 14.545 23446 Z= 0.243 Chirality : 0.038 0.470 2909 Planarity : 0.004 0.047 2996 Dihedral : 3.328 16.501 2515 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.93 % Allowed : 14.62 % Favored : 83.45 % 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: 2.09 (0.18), residues: 2358 helix: 2.46 (0.13), residues: 1574 sheet: -2.68 (0.61), residues: 65 loop : -0.71 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 144 HIS 0.003 0.000 HIS D1108 PHE 0.016 0.001 PHE C 402 TYR 0.019 0.001 TYR D 878 ARG 0.006 0.000 ARG C 741 Details of bonding type rmsd hydrogen bonds : bond 0.03654 ( 1094) hydrogen bonds : angle 3.37776 ( 3219) metal coordination : bond 0.00159 ( 11) metal coordination : angle 0.93048 ( 6) covalent geometry : bond 0.00205 (17168) covalent geometry : angle 0.47730 (23440) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 344 time to evaluate : 1.722 Fit side-chains revert: symmetry clash REVERT: C 30 GLN cc_start: 0.8576 (tt0) cc_final: 0.8356 (tt0) REVERT: C 44 GLU cc_start: 0.8107 (tp30) cc_final: 0.7673 (tp30) REVERT: C 97 LYS cc_start: 0.8900 (ttmm) cc_final: 0.8651 (ttmm) REVERT: C 124 GLU cc_start: 0.7913 (tp30) cc_final: 0.7638 (mm-30) REVERT: C 131 LYS cc_start: 0.8558 (tppp) cc_final: 0.8266 (tppp) REVERT: C 146 ARG cc_start: 0.7689 (mtm110) cc_final: 0.7445 (mtm110) REVERT: C 170 CYS cc_start: 0.8112 (m) cc_final: 0.7898 (m) REVERT: C 199 ARG cc_start: 0.8409 (mtp180) cc_final: 0.8189 (mmm-85) REVERT: C 259 GLU cc_start: 0.7400 (mp0) cc_final: 0.7103 (mp0) REVERT: C 478 ASN cc_start: 0.8196 (p0) cc_final: 0.7796 (p0) REVERT: C 509 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8149 (mt0) REVERT: C 563 TYR cc_start: 0.8080 (t80) cc_final: 0.7850 (t80) REVERT: C 573 ARG cc_start: 0.7829 (mmp80) cc_final: 0.7584 (mmp80) REVERT: C 641 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.8089 (mp10) REVERT: C 697 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7424 (mt-10) REVERT: D 185 THR cc_start: 0.8834 (p) cc_final: 0.8482 (t) REVERT: D 290 VAL cc_start: 0.8109 (m) cc_final: 0.7859 (p) REVERT: D 457 MET cc_start: 0.8290 (tpp) cc_final: 0.7817 (tpp) REVERT: D 485 ASN cc_start: 0.7601 (p0) cc_final: 0.7385 (p0) REVERT: D 496 ASP cc_start: 0.7707 (m-30) cc_final: 0.7364 (m-30) REVERT: D 689 MET cc_start: 0.6875 (OUTLIER) cc_final: 0.6597 (ptp) REVERT: D 769 ASN cc_start: 0.7706 (t0) cc_final: 0.7272 (t0) REVERT: D 857 LEU cc_start: 0.8631 (tp) cc_final: 0.8316 (tt) REVERT: D 1059 ARG cc_start: 0.7504 (ttp80) cc_final: 0.7290 (ttp80) REVERT: D 1083 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.8052 (mtpt) REVERT: D 1099 ARG cc_start: 0.8410 (mmm-85) cc_final: 0.8129 (mmt180) REVERT: D 1177 MET cc_start: 0.8042 (mmm) cc_final: 0.7815 (mmm) REVERT: D 1195 MET cc_start: 0.7544 (tpp) cc_final: 0.7118 (tpp) outliers start: 30 outliers final: 17 residues processed: 356 average time/residue: 0.3224 time to fit residues: 165.8202 Evaluate side-chains 355 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 334 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 509 GLN Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 586 SER Chi-restraints excluded: chain C residue 641 GLN Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 689 MET Chi-restraints excluded: chain D residue 901 SER Chi-restraints excluded: chain D residue 922 VAL Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 967 LEU Chi-restraints excluded: chain D residue 1012 LEU Chi-restraints excluded: chain D residue 1083 LYS Chi-restraints excluded: chain D residue 1089 MET Chi-restraints excluded: chain D residue 1142 LEU Chi-restraints excluded: chain F residue 96 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 28 optimal weight: 1.9990 chunk 231 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 180 optimal weight: 0.6980 chunk 234 optimal weight: 50.0000 chunk 40 optimal weight: 0.5980 chunk 208 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 57 optimal weight: 0.0000 chunk 103 optimal weight: 0.8980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 141 ASN C 272 GLN C 494 GLN D 792 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.130889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.103621 restraints weight = 26394.054| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.85 r_work: 0.3118 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 17179 Z= 0.111 Angle : 0.490 14.700 23446 Z= 0.248 Chirality : 0.039 0.504 2909 Planarity : 0.004 0.046 2996 Dihedral : 3.264 16.261 2515 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.67 % Allowed : 15.58 % Favored : 82.74 % 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: 2.05 (0.18), residues: 2358 helix: 2.46 (0.13), residues: 1583 sheet: -2.73 (0.60), residues: 65 loop : -0.82 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 144 HIS 0.003 0.001 HIS D 792 PHE 0.020 0.001 PHE C 402 TYR 0.017 0.001 TYR D 878 ARG 0.008 0.000 ARG C 242 Details of bonding type rmsd hydrogen bonds : bond 0.03988 ( 1094) hydrogen bonds : angle 3.38376 ( 3219) metal coordination : bond 0.00263 ( 11) metal coordination : angle 0.98183 ( 6) covalent geometry : bond 0.00255 (17168) covalent geometry : angle 0.48943 (23440) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 338 time to evaluate : 1.747 Fit side-chains revert: symmetry clash REVERT: C 30 GLN cc_start: 0.8602 (tt0) cc_final: 0.8386 (tt0) REVERT: C 97 LYS cc_start: 0.8913 (ttmm) cc_final: 0.8590 (ttmm) REVERT: C 124 GLU cc_start: 0.7934 (tp30) cc_final: 0.7656 (mm-30) REVERT: C 131 LYS cc_start: 0.8575 (tppp) cc_final: 0.8275 (tppp) REVERT: C 146 ARG cc_start: 0.7720 (mtm110) cc_final: 0.7495 (mtm110) REVERT: C 170 CYS cc_start: 0.8137 (m) cc_final: 0.7889 (m) REVERT: C 199 ARG cc_start: 0.8449 (mtp180) cc_final: 0.8231 (mmm-85) REVERT: C 259 GLU cc_start: 0.7446 (mp0) cc_final: 0.7096 (mp0) REVERT: C 478 ASN cc_start: 0.8222 (p0) cc_final: 0.7838 (p0) REVERT: C 494 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.7952 (tp40) REVERT: C 509 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8126 (mt0) REVERT: C 563 TYR cc_start: 0.8078 (t80) cc_final: 0.7852 (t80) REVERT: C 573 ARG cc_start: 0.7856 (mmp80) cc_final: 0.7635 (mmp80) REVERT: C 641 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.8138 (mp10) REVERT: C 697 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7456 (mt-10) REVERT: D 185 THR cc_start: 0.8832 (p) cc_final: 0.8495 (t) REVERT: D 290 VAL cc_start: 0.8075 (m) cc_final: 0.7843 (p) REVERT: D 457 MET cc_start: 0.8275 (tpp) cc_final: 0.7790 (tpp) REVERT: D 485 ASN cc_start: 0.7535 (p0) cc_final: 0.7330 (p0) REVERT: D 496 ASP cc_start: 0.7765 (m-30) cc_final: 0.7418 (m-30) REVERT: D 689 MET cc_start: 0.6914 (OUTLIER) cc_final: 0.6644 (ptp) REVERT: D 769 ASN cc_start: 0.7724 (t0) cc_final: 0.7291 (t0) REVERT: D 857 LEU cc_start: 0.8640 (tp) cc_final: 0.8331 (tt) REVERT: D 971 LYS cc_start: 0.8629 (tttm) cc_final: 0.8380 (tttp) REVERT: D 1083 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8101 (mtpt) REVERT: D 1099 ARG cc_start: 0.8452 (mmm-85) cc_final: 0.8174 (mmt180) REVERT: D 1177 MET cc_start: 0.8032 (mmm) cc_final: 0.7738 (mmm) outliers start: 26 outliers final: 15 residues processed: 350 average time/residue: 0.3207 time to fit residues: 161.5234 Evaluate side-chains 352 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 332 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 509 GLN Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 586 SER Chi-restraints excluded: chain C residue 641 GLN Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 689 MET Chi-restraints excluded: chain D residue 901 SER Chi-restraints excluded: chain D residue 922 VAL Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 967 LEU Chi-restraints excluded: chain D residue 1012 LEU Chi-restraints excluded: chain D residue 1083 LYS Chi-restraints excluded: chain D residue 1089 MET Chi-restraints excluded: chain D residue 1142 LEU Chi-restraints excluded: chain F residue 96 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 58 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 202 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 149 optimal weight: 0.0970 chunk 133 optimal weight: 2.9990 chunk 50 optimal weight: 0.0040 chunk 39 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 chunk 233 optimal weight: 30.0000 chunk 110 optimal weight: 1.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 141 ASN ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.131665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.104488 restraints weight = 26763.139| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.89 r_work: 0.3112 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17179 Z= 0.106 Angle : 0.498 16.414 23446 Z= 0.250 Chirality : 0.039 0.486 2909 Planarity : 0.004 0.046 2996 Dihedral : 3.256 16.182 2515 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.48 % Allowed : 15.90 % Favored : 82.61 % 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: 2.08 (0.18), residues: 2358 helix: 2.47 (0.13), residues: 1583 sheet: -2.70 (0.60), residues: 65 loop : -0.80 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 144 HIS 0.004 0.001 HIS D1108 PHE 0.019 0.001 PHE C 402 TYR 0.015 0.001 TYR C 32 ARG 0.007 0.000 ARG D1059 Details of bonding type rmsd hydrogen bonds : bond 0.03859 ( 1094) hydrogen bonds : angle 3.36999 ( 3219) metal coordination : bond 0.00204 ( 11) metal coordination : angle 0.96448 ( 6) covalent geometry : bond 0.00237 (17168) covalent geometry : angle 0.49781 (23440) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 340 time to evaluate : 1.639 Fit side-chains revert: symmetry clash REVERT: C 30 GLN cc_start: 0.8590 (tt0) cc_final: 0.8376 (tt0) REVERT: C 97 LYS cc_start: 0.8890 (ttmm) cc_final: 0.8567 (ttmm) REVERT: C 124 GLU cc_start: 0.7941 (tp30) cc_final: 0.7672 (mm-30) REVERT: C 131 LYS cc_start: 0.8584 (tppp) cc_final: 0.8284 (tppp) REVERT: C 146 ARG cc_start: 0.7703 (mtm110) cc_final: 0.7446 (mtm110) REVERT: C 170 CYS cc_start: 0.8141 (m) cc_final: 0.7891 (m) REVERT: C 199 ARG cc_start: 0.8434 (mtp180) cc_final: 0.8223 (mmm-85) REVERT: C 259 GLU cc_start: 0.7472 (mp0) cc_final: 0.7067 (mp0) REVERT: C 478 ASN cc_start: 0.8218 (p0) cc_final: 0.7821 (p0) REVERT: C 509 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8157 (mt0) REVERT: C 573 ARG cc_start: 0.7831 (mmp80) cc_final: 0.7623 (mmp80) REVERT: C 641 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.8120 (mp10) REVERT: C 697 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7460 (mt-10) REVERT: D 137 ARG cc_start: 0.8574 (mmm-85) cc_final: 0.8239 (mtt90) REVERT: D 185 THR cc_start: 0.8841 (p) cc_final: 0.8502 (t) REVERT: D 290 VAL cc_start: 0.8045 (m) cc_final: 0.7817 (p) REVERT: D 457 MET cc_start: 0.8256 (tpp) cc_final: 0.7769 (tpp) REVERT: D 496 ASP cc_start: 0.7754 (m-30) cc_final: 0.7393 (m-30) REVERT: D 689 MET cc_start: 0.6895 (OUTLIER) cc_final: 0.6616 (ptp) REVERT: D 769 ASN cc_start: 0.7728 (t0) cc_final: 0.7288 (t0) REVERT: D 857 LEU cc_start: 0.8595 (tp) cc_final: 0.8285 (tt) REVERT: D 971 LYS cc_start: 0.8630 (tttm) cc_final: 0.8373 (tttp) REVERT: D 1083 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8072 (mtpt) REVERT: D 1099 ARG cc_start: 0.8444 (mmm-85) cc_final: 0.8166 (mmt180) REVERT: D 1177 MET cc_start: 0.8059 (mmm) cc_final: 0.7785 (mmm) REVERT: D 1195 MET cc_start: 0.7532 (tpp) cc_final: 0.7114 (tpp) outliers start: 23 outliers final: 16 residues processed: 349 average time/residue: 0.3219 time to fit residues: 162.3579 Evaluate side-chains 356 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 336 time to evaluate : 1.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 382 MET Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 509 GLN Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 586 SER Chi-restraints excluded: chain C residue 641 GLN Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 689 MET Chi-restraints excluded: chain D residue 901 SER Chi-restraints excluded: chain D residue 922 VAL Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 967 LEU Chi-restraints excluded: chain D residue 1012 LEU Chi-restraints excluded: chain D residue 1083 LYS Chi-restraints excluded: chain D residue 1089 MET Chi-restraints excluded: chain D residue 1142 LEU Chi-restraints excluded: chain F residue 96 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 39 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 180 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 139 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 151 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 223 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 141 ASN ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 GLN ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.129921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.102468 restraints weight = 26567.457| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.86 r_work: 0.3106 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17179 Z= 0.124 Angle : 0.515 15.522 23446 Z= 0.260 Chirality : 0.040 0.502 2909 Planarity : 0.004 0.046 2996 Dihedral : 3.292 16.254 2515 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.48 % Allowed : 16.29 % Favored : 82.23 % 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: 2.05 (0.18), residues: 2358 helix: 2.47 (0.13), residues: 1579 sheet: -2.71 (0.60), residues: 65 loop : -0.85 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 144 HIS 0.004 0.001 HIS D 173 PHE 0.021 0.001 PHE C 402 TYR 0.018 0.001 TYR C 32 ARG 0.007 0.001 ARG C 242 Details of bonding type rmsd hydrogen bonds : bond 0.04302 ( 1094) hydrogen bonds : angle 3.42742 ( 3219) metal coordination : bond 0.00393 ( 11) metal coordination : angle 1.08659 ( 6) covalent geometry : bond 0.00289 (17168) covalent geometry : angle 0.51500 (23440) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 342 time to evaluate : 1.900 Fit side-chains revert: symmetry clash REVERT: C 30 GLN cc_start: 0.8605 (tt0) cc_final: 0.8388 (tt0) REVERT: C 97 LYS cc_start: 0.8892 (ttmm) cc_final: 0.8663 (ttmm) REVERT: C 124 GLU cc_start: 0.7947 (tp30) cc_final: 0.7649 (mm-30) REVERT: C 131 LYS cc_start: 0.8593 (tppp) cc_final: 0.8286 (tppp) REVERT: C 144 TRP cc_start: 0.8505 (t60) cc_final: 0.7759 (t60) REVERT: C 146 ARG cc_start: 0.7711 (mtm110) cc_final: 0.7483 (mtm110) REVERT: C 170 CYS cc_start: 0.8171 (m) cc_final: 0.7914 (m) REVERT: C 259 GLU cc_start: 0.7519 (mp0) cc_final: 0.7114 (mp0) REVERT: C 478 ASN cc_start: 0.8238 (p0) cc_final: 0.7854 (p0) REVERT: C 509 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8134 (mt0) REVERT: C 573 ARG cc_start: 0.7857 (mmp80) cc_final: 0.7648 (mmp80) REVERT: C 641 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.8146 (mp10) REVERT: C 697 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7502 (mt-10) REVERT: D 93 THR cc_start: 0.9031 (m) cc_final: 0.8808 (t) REVERT: D 137 ARG cc_start: 0.8588 (mmm-85) cc_final: 0.8094 (mtt90) REVERT: D 185 THR cc_start: 0.8846 (p) cc_final: 0.8512 (t) REVERT: D 290 VAL cc_start: 0.8048 (m) cc_final: 0.7845 (p) REVERT: D 457 MET cc_start: 0.8255 (tpp) cc_final: 0.7754 (tpp) REVERT: D 496 ASP cc_start: 0.7763 (m-30) cc_final: 0.7418 (m-30) REVERT: D 689 MET cc_start: 0.6953 (OUTLIER) cc_final: 0.6690 (ptp) REVERT: D 769 ASN cc_start: 0.7703 (t0) cc_final: 0.7243 (t0) REVERT: D 857 LEU cc_start: 0.8589 (tp) cc_final: 0.8289 (tt) REVERT: D 971 LYS cc_start: 0.8641 (tttm) cc_final: 0.8392 (tttp) REVERT: D 1083 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8093 (mtpt) REVERT: D 1177 MET cc_start: 0.8058 (mmm) cc_final: 0.7796 (mmm) REVERT: D 1195 MET cc_start: 0.7557 (tpp) cc_final: 0.7144 (tpp) outliers start: 23 outliers final: 15 residues processed: 353 average time/residue: 0.3217 time to fit residues: 164.0298 Evaluate side-chains 356 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 337 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 509 GLN Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 536 SER Chi-restraints excluded: chain C residue 586 SER Chi-restraints excluded: chain C residue 641 GLN Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 689 MET Chi-restraints excluded: chain D residue 901 SER Chi-restraints excluded: chain D residue 922 VAL Chi-restraints excluded: chain D residue 940 CYS Chi-restraints excluded: chain D residue 967 LEU Chi-restraints excluded: chain D residue 1012 LEU Chi-restraints excluded: chain D residue 1083 LYS Chi-restraints excluded: chain D residue 1089 MET Chi-restraints excluded: chain D residue 1142 LEU Chi-restraints excluded: chain F residue 96 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 196 optimal weight: 5.9990 chunk 100 optimal weight: 0.0770 chunk 34 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 132 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 208 optimal weight: 6.9990 chunk 88 optimal weight: 0.5980 chunk 221 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 141 ASN ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.131879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.104806 restraints weight = 26256.345| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.73 r_work: 0.3152 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17179 Z= 0.112 Angle : 0.513 16.660 23446 Z= 0.257 Chirality : 0.039 0.504 2909 Planarity : 0.004 0.046 2996 Dihedral : 3.273 16.161 2515 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.48 % Allowed : 16.55 % Favored : 81.97 % 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: 2.08 (0.18), residues: 2358 helix: 2.48 (0.13), residues: 1580 sheet: -2.71 (0.59), residues: 65 loop : -0.80 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 144 HIS 0.003 0.001 HIS D 173 PHE 0.020 0.001 PHE C 402 TYR 0.016 0.001 TYR C 32 ARG 0.008 0.001 ARG C 242 Details of bonding type rmsd hydrogen bonds : bond 0.03968 ( 1094) hydrogen bonds : angle 3.38763 ( 3219) metal coordination : bond 0.00241 ( 11) metal coordination : angle 1.02545 ( 6) covalent geometry : bond 0.00257 (17168) covalent geometry : angle 0.51244 (23440) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9982.81 seconds wall clock time: 172 minutes 37.39 seconds (10357.39 seconds total)