Starting phenix.real_space_refine on Sun Aug 24 04:07:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cdk_16576/08_2025/8cdk_16576.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cdk_16576/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8cdk_16576/08_2025/8cdk_16576.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cdk_16576/08_2025/8cdk_16576.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cdk_16576/08_2025/8cdk_16576.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cdk_16576/08_2025/8cdk_16576.map" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ASP:plan': 10, 'GLN:plan1': 8, 'ARG:plan': 6, 'GLU:plan': 15, 'ASN:plan1': 3, 'PHE:plan': 2, 'TYR:plan': 3} 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: {'TYR:plan': 1, 'GLU:plan': 50, 'ASP:plan': 25, 'ARG:plan': 8, 'ASN:plan1': 2, 'GLN:plan1': 6, 'HIS:plan': 1} 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: {'ARG:plan': 2, 'GLU:plan': 5, 'ASP:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1} 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: {'ASP:plan': 10, 'GLU:plan': 13, 'PHE:plan': 5, 'GLN:plan1': 6, 'ASN:plan1': 6, 'HIS:plan': 1, 'ARG:plan': 2, 'TRP:plan': 1} 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: {'ASP:plan': 16, 'GLU:plan': 15, 'ARG:plan': 15, 'TYR:plan': 4, 'GLN:plan1': 16, 'ASN:plan1': 14, 'HIS:plan': 10, 'PHE:plan': 13, 'TRP:plan': 2} 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: 4.13, per 1000 atoms: 0.24 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: 1.59 Conformation dependent library (CDL) restraints added in 831.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.73 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: 3.33 Time building geometry restraints manager: 2.06 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.860 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.010 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.000 ARG D1042 TYR 0.017 0.001 TYR D1117 PHE 0.017 0.001 PHE C 402 TRP 0.010 0.001 TRP C 545 HIS 0.005 0.001 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00262 (17168) covalent geometry : angle 0.56579 (23440) hydrogen bonds : bond 0.18466 ( 1094) hydrogen bonds : angle 4.89365 ( 3219) metal coordination : bond 0.08336 ( 11) metal coordination : angle 4.68766 ( 6) *********************** 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 : 0.649 Fit side-chains 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: 0.8258 (ttmm) REVERT: C 117 LYS cc_start: 0.7695 (mtpp) cc_final: 0.7410 (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: 0.8032 (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: 0.8061 (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: 0.8021 (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 1010 ASP cc_start: 0.6863 (p0) cc_final: 0.6560 (p0) 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: 0.1461 time to fit residues: 82.4676 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 : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 40.0000 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 50.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3659 r_free = 0.3659 target = 0.130323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.103123 restraints weight = 26271.131| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.78 r_work: 0.3102 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17179 Z= 0.148 Angle : 0.537 8.249 23446 Z= 0.282 Chirality : 0.040 0.167 2909 Planarity : 0.004 0.059 2996 Dihedral : 3.587 16.123 2515 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.35 % Allowed : 6.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.18), residues: 2358 helix: 2.21 (0.13), residues: 1550 sheet: -2.78 (0.61), residues: 65 loop : -0.97 (0.22), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1042 TYR 0.016 0.002 TYR C 377 PHE 0.024 0.001 PHE C 402 TRP 0.009 0.001 TRP S 61 HIS 0.004 0.001 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00328 (17168) covalent geometry : angle 0.53623 (23440) hydrogen bonds : bond 0.05450 ( 1094) hydrogen bonds : angle 3.93519 ( 3219) metal coordination : bond 0.00914 ( 11) metal coordination : angle 1.20899 ( 6) *********************** 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 375 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 354 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: C 30 GLN cc_start: 0.8637 (tt0) cc_final: 0.8419 (tt0) REVERT: C 44 GLU cc_start: 0.8159 (tp30) cc_final: 0.7917 (tp30) REVERT: C 97 LYS cc_start: 0.8944 (ttmm) cc_final: 0.8635 (ttmm) REVERT: C 124 GLU cc_start: 0.7887 (tp30) cc_final: 0.7645 (mm-30) REVERT: C 131 LYS cc_start: 0.8456 (tppp) cc_final: 0.8242 (tppp) REVERT: C 170 CYS cc_start: 0.8095 (m) cc_final: 0.7877 (m) REVERT: C 199 ARG cc_start: 0.8477 (tpp80) cc_final: 0.8252 (ttm110) REVERT: C 372 ASP cc_start: 0.7951 (m-30) cc_final: 0.7725 (m-30) REVERT: C 478 ASN cc_start: 0.8170 (p0) cc_final: 0.7805 (p0) REVERT: C 509 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.8170 (mt0) REVERT: C 694 GLN cc_start: 0.7862 (mm-40) cc_final: 0.7651 (mm-40) REVERT: C 697 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7437 (mt-10) REVERT: D 35 GLN cc_start: 0.7729 (mt0) cc_final: 0.7458 (mt0) REVERT: D 70 LYS cc_start: 0.8218 (mttp) cc_final: 0.7912 (mttp) REVERT: D 496 ASP cc_start: 0.7714 (m-30) cc_final: 0.7407 (m-30) REVERT: D 769 ASN cc_start: 0.7661 (t0) cc_final: 0.7307 (t0) REVERT: D 971 LYS cc_start: 0.8466 (mmmt) cc_final: 0.8129 (tptp) REVERT: D 1195 MET cc_start: 0.7512 (tpp) cc_final: 0.7242 (tpp) outliers start: 21 outliers final: 8 residues processed: 364 average time/residue: 0.1505 time to fit residues: 79.4194 Evaluate side-chains 341 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 332 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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 901 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 212 optimal weight: 30.0000 chunk 231 optimal weight: 6.9990 chunk 32 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 175 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 141 ASN R 76 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.126935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.099741 restraints weight = 26716.223| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.86 r_work: 0.3040 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 17179 Z= 0.230 Angle : 0.571 7.993 23446 Z= 0.302 Chirality : 0.043 0.204 2909 Planarity : 0.004 0.051 2996 Dihedral : 3.789 17.262 2515 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.80 % Allowed : 9.72 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.18), residues: 2358 helix: 2.03 (0.13), residues: 1566 sheet: -2.78 (0.61), residues: 65 loop : -1.05 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D1059 TYR 0.019 0.002 TYR C 377 PHE 0.028 0.002 PHE C 402 TRP 0.012 0.002 TRP S 61 HIS 0.009 0.001 HIS D 707 Details of bonding type rmsd covalent geometry : bond 0.00549 (17168) covalent geometry : angle 0.57052 (23440) hydrogen bonds : bond 0.06595 ( 1094) hydrogen bonds : angle 3.97649 ( 3219) metal coordination : bond 0.01261 ( 11) metal coordination : angle 1.69666 ( 6) *********************** 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 386 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 358 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: C 44 GLU cc_start: 0.8156 (tp30) cc_final: 0.7744 (tp30) REVERT: C 124 GLU cc_start: 0.7991 (tp30) cc_final: 0.7655 (mm-30) REVERT: C 131 LYS cc_start: 0.8486 (tppp) cc_final: 0.8188 (tppp) REVERT: C 170 CYS cc_start: 0.8251 (m) cc_final: 0.7963 (m) REVERT: C 199 ARG cc_start: 0.8502 (tpp80) cc_final: 0.8203 (mtp180) REVERT: C 448 GLN cc_start: 0.8592 (mm-40) cc_final: 0.8366 (mm-40) REVERT: C 478 ASN cc_start: 0.8363 (p0) cc_final: 0.7971 (p0) REVERT: C 509 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8112 (mt0) REVERT: C 563 TYR cc_start: 0.8192 (t80) cc_final: 0.7965 (t80) REVERT: C 573 ARG cc_start: 0.7903 (mmp80) cc_final: 0.7607 (mmp80) REVERT: C 641 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8018 (mp10) REVERT: C 690 THR cc_start: 0.8493 (m) cc_final: 0.8283 (p) REVERT: D 78 LYS cc_start: 0.8270 (mmmm) cc_final: 0.8037 (mmmm) REVERT: D 185 THR cc_start: 0.8852 (p) cc_final: 0.8498 (t) REVERT: D 457 MET cc_start: 0.8427 (mmm) cc_final: 0.7866 (tpp) REVERT: D 496 ASP cc_start: 0.7838 (m-30) cc_final: 0.7515 (m-30) REVERT: D 577 LYS cc_start: 0.8339 (ptpt) cc_final: 0.8093 (pttt) REVERT: D 769 ASN cc_start: 0.7644 (t0) cc_final: 0.7236 (t0) REVERT: D 857 LEU cc_start: 0.8780 (tp) cc_final: 0.8416 (tt) REVERT: D 971 LYS cc_start: 0.8644 (mmmt) cc_final: 0.8391 (tttp) REVERT: D 1099 ARG cc_start: 0.8459 (mmm-85) cc_final: 0.8199 (mmt180) REVERT: D 1195 MET cc_start: 0.7501 (tpp) cc_final: 0.7152 (tpp) outliers start: 28 outliers final: 14 residues processed: 368 average time/residue: 0.1459 time to fit residues: 78.3274 Evaluate side-chains 365 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 349 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 641 GLN Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 225 ASN Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 288 LYS 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 D residue 1004 LEU Chi-restraints excluded: chain D residue 1127 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 128 optimal weight: 0.1980 chunk 34 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 180 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 134 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 157 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 227 optimal weight: 30.0000 chunk 163 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 141 ASN C 361 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.130003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.102826 restraints weight = 26463.982| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.88 r_work: 0.3093 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17179 Z= 0.122 Angle : 0.493 7.565 23446 Z= 0.257 Chirality : 0.039 0.150 2909 Planarity : 0.004 0.048 2996 Dihedral : 3.584 16.839 2515 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.00 % Allowed : 12.23 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.18), residues: 2358 helix: 2.25 (0.13), residues: 1563 sheet: -2.73 (0.62), residues: 65 loop : -0.98 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 741 TYR 0.016 0.001 TYR C 377 PHE 0.021 0.001 PHE C 402 TRP 0.011 0.001 TRP R 33 HIS 0.004 0.001 HIS D 707 Details of bonding type rmsd covalent geometry : bond 0.00272 (17168) covalent geometry : angle 0.49290 (23440) hydrogen bonds : bond 0.04709 ( 1094) hydrogen bonds : angle 3.65424 ( 3219) metal coordination : bond 0.00369 ( 11) metal coordination : angle 1.17056 ( 6) *********************** 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 381 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 350 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 44 GLU cc_start: 0.8128 (tp30) cc_final: 0.7832 (tp30) REVERT: C 97 LYS cc_start: 0.8956 (ttmm) cc_final: 0.8679 (ttmm) REVERT: C 124 GLU cc_start: 0.7935 (tp30) cc_final: 0.7612 (mm-30) REVERT: C 131 LYS cc_start: 0.8516 (tppp) cc_final: 0.8234 (tppp) REVERT: C 170 CYS cc_start: 0.8149 (m) cc_final: 0.7909 (m) REVERT: C 199 ARG cc_start: 0.8377 (tpp80) cc_final: 0.8131 (mmm-85) REVERT: C 478 ASN cc_start: 0.8292 (p0) cc_final: 0.7897 (p0) REVERT: C 509 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8133 (mt0) REVERT: C 563 TYR cc_start: 0.8156 (t80) cc_final: 0.7899 (t80) REVERT: C 641 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.7996 (mp10) REVERT: D 78 LYS cc_start: 0.8275 (mmmm) cc_final: 0.8033 (mmmm) REVERT: D 185 THR cc_start: 0.8811 (p) cc_final: 0.8465 (t) REVERT: D 457 MET cc_start: 0.8330 (mmm) cc_final: 0.7978 (tpp) REVERT: D 496 ASP cc_start: 0.7754 (m-30) cc_final: 0.7409 (m-30) REVERT: D 691 ASP cc_start: 0.7205 (m-30) cc_final: 0.6885 (m-30) REVERT: D 737 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7998 (mm-30) REVERT: D 769 ASN cc_start: 0.7676 (t0) cc_final: 0.7262 (t0) REVERT: D 857 LEU cc_start: 0.8701 (tp) cc_final: 0.8356 (tt) REVERT: D 971 LYS cc_start: 0.8638 (mmmt) cc_final: 0.8381 (tttp) REVERT: D 1059 ARG cc_start: 0.7455 (ttp80) cc_final: 0.7077 (ttp80) REVERT: D 1083 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8028 (mtpt) REVERT: D 1099 ARG cc_start: 0.8403 (mmm-85) cc_final: 0.8132 (mmt180) REVERT: D 1195 MET cc_start: 0.7424 (tpp) cc_final: 0.6973 (tpp) outliers start: 31 outliers final: 14 residues processed: 359 average time/residue: 0.1486 time to fit residues: 77.6603 Evaluate side-chains 357 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 340 time to evaluate : 0.678 ------------------------------------------------------------------------------- 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 146 GLU Chi-restraints excluded: chain D residue 225 ASN Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 266 VAL 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 1012 LEU Chi-restraints excluded: chain D residue 1083 LYS Chi-restraints excluded: chain D residue 1142 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 79 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 171 optimal weight: 0.2980 chunk 187 optimal weight: 3.9990 chunk 226 optimal weight: 10.0000 chunk 192 optimal weight: 3.9990 chunk 107 optimal weight: 0.0970 chunk 190 optimal weight: 0.1980 chunk 77 optimal weight: 0.5980 chunk 118 optimal weight: 0.9990 chunk 220 optimal weight: 6.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.3669 r_free = 0.3669 target = 0.131359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.104224 restraints weight = 26447.408| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.87 r_work: 0.3103 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17179 Z= 0.106 Angle : 0.475 7.745 23446 Z= 0.245 Chirality : 0.038 0.258 2909 Planarity : 0.004 0.048 2996 Dihedral : 3.432 16.697 2515 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.80 % Allowed : 13.78 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.18), residues: 2358 helix: 2.37 (0.14), residues: 1571 sheet: -2.73 (0.61), residues: 65 loop : -0.90 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 741 TYR 0.018 0.001 TYR D 878 PHE 0.019 0.001 PHE C 402 TRP 0.010 0.001 TRP R 33 HIS 0.003 0.001 HIS D 707 Details of bonding type rmsd covalent geometry : bond 0.00228 (17168) covalent geometry : angle 0.47443 (23440) hydrogen bonds : bond 0.04026 ( 1094) hydrogen bonds : angle 3.49211 ( 3219) metal coordination : bond 0.00187 ( 11) metal coordination : angle 0.98450 ( 6) *********************** 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 378 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 350 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 44 GLU cc_start: 0.8106 (tp30) cc_final: 0.7638 (tp30) REVERT: C 97 LYS cc_start: 0.8936 (ttmm) cc_final: 0.8672 (ttmm) REVERT: C 124 GLU cc_start: 0.7943 (tp30) cc_final: 0.7643 (mm-30) REVERT: C 131 LYS cc_start: 0.8555 (tppp) cc_final: 0.8271 (tppp) REVERT: C 170 CYS cc_start: 0.8132 (m) cc_final: 0.7904 (m) REVERT: C 478 ASN cc_start: 0.8253 (p0) cc_final: 0.7864 (p0) REVERT: C 494 GLN cc_start: 0.8414 (tp40) cc_final: 0.8136 (tp40) REVERT: C 509 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8157 (mt0) REVERT: C 641 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.8074 (mp10) REVERT: D 177 LEU cc_start: 0.8442 (tt) cc_final: 0.8211 (tt) REVERT: D 185 THR cc_start: 0.8823 (p) cc_final: 0.8473 (t) REVERT: D 457 MET cc_start: 0.8308 (mmm) cc_final: 0.7970 (tpp) REVERT: D 485 ASN cc_start: 0.7879 (p0) cc_final: 0.7550 (p0) REVERT: D 496 ASP cc_start: 0.7727 (m-30) cc_final: 0.7378 (m-30) REVERT: D 538 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7845 (tp30) REVERT: D 737 GLU cc_start: 0.8204 (mm-30) cc_final: 0.8002 (mm-30) REVERT: D 769 ASN cc_start: 0.7673 (t0) cc_final: 0.7272 (t0) REVERT: D 857 LEU cc_start: 0.8665 (tp) cc_final: 0.8341 (tt) REVERT: D 971 LYS cc_start: 0.8609 (mmmt) cc_final: 0.8335 (tttp) REVERT: D 1059 ARG cc_start: 0.7485 (ttp80) cc_final: 0.7182 (ttp80) REVERT: D 1099 ARG cc_start: 0.8398 (mmm-85) cc_final: 0.8124 (mmt180) REVERT: D 1174 ARG cc_start: 0.7946 (mtm-85) cc_final: 0.7715 (mtt-85) REVERT: D 1195 MET cc_start: 0.7504 (tpp) cc_final: 0.7193 (tpp) outliers start: 28 outliers final: 18 residues processed: 362 average time/residue: 0.1502 time to fit residues: 79.3045 Evaluate side-chains 359 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 339 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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 95 MET Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 225 ASN Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 288 LYS 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 1012 LEU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 151 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 193 optimal weight: 10.0000 chunk 78 optimal weight: 0.6980 chunk 137 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 141 ASN D 792 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.129216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.101978 restraints weight = 26446.641| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.87 r_work: 0.3080 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17179 Z= 0.154 Angle : 0.504 8.080 23446 Z= 0.261 Chirality : 0.040 0.183 2909 Planarity : 0.004 0.048 2996 Dihedral : 3.461 16.668 2515 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.80 % Allowed : 14.94 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.18), residues: 2358 helix: 2.30 (0.13), residues: 1572 sheet: -2.75 (0.60), residues: 65 loop : -0.89 (0.22), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 741 TYR 0.018 0.002 TYR C 278 PHE 0.025 0.001 PHE C 402 TRP 0.010 0.001 TRP R 33 HIS 0.005 0.001 HIS D 707 Details of bonding type rmsd covalent geometry : bond 0.00365 (17168) covalent geometry : angle 0.50364 (23440) hydrogen bonds : bond 0.04943 ( 1094) hydrogen bonds : angle 3.58261 ( 3219) metal coordination : bond 0.00681 ( 11) metal coordination : angle 1.15347 ( 6) *********************** 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 382 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 354 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 44 GLU cc_start: 0.8092 (tp30) cc_final: 0.7655 (tp30) REVERT: C 124 GLU cc_start: 0.7956 (tp30) cc_final: 0.7644 (mm-30) REVERT: C 131 LYS cc_start: 0.8580 (tppp) cc_final: 0.8269 (tppp) REVERT: C 170 CYS cc_start: 0.8184 (m) cc_final: 0.7915 (m) REVERT: C 199 ARG cc_start: 0.8435 (mmm-85) cc_final: 0.8089 (mmm-85) REVERT: C 478 ASN cc_start: 0.8292 (p0) cc_final: 0.7886 (p0) REVERT: C 494 GLN cc_start: 0.8447 (tp40) cc_final: 0.8164 (tp40) REVERT: C 509 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8145 (mt0) REVERT: C 641 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.8093 (mp10) REVERT: D 177 LEU cc_start: 0.8493 (tt) cc_final: 0.8263 (tt) REVERT: D 185 THR cc_start: 0.8849 (p) cc_final: 0.8506 (t) REVERT: D 457 MET cc_start: 0.8374 (mmm) cc_final: 0.8009 (tpp) REVERT: D 485 ASN cc_start: 0.7978 (p0) cc_final: 0.7691 (p0) REVERT: D 496 ASP cc_start: 0.7812 (m-30) cc_final: 0.7468 (m-30) REVERT: D 689 MET cc_start: 0.7189 (ptp) cc_final: 0.6944 (ptp) REVERT: D 738 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8343 (mp) REVERT: D 769 ASN cc_start: 0.7732 (t0) cc_final: 0.7271 (t0) REVERT: D 857 LEU cc_start: 0.8681 (tp) cc_final: 0.8357 (tt) REVERT: D 971 LYS cc_start: 0.8607 (mmmt) cc_final: 0.8353 (tttp) REVERT: D 1059 ARG cc_start: 0.7517 (ttp80) cc_final: 0.7211 (ttp80) REVERT: D 1099 ARG cc_start: 0.8445 (mmm-85) cc_final: 0.8176 (mmt180) REVERT: D 1174 ARG cc_start: 0.7956 (mtm-85) cc_final: 0.7613 (mtt180) REVERT: D 1177 MET cc_start: 0.8094 (mmm) cc_final: 0.7821 (mmm) outliers start: 28 outliers final: 22 residues processed: 363 average time/residue: 0.1268 time to fit residues: 67.7896 Evaluate side-chains 368 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 343 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 586 SER Chi-restraints excluded: chain C residue 641 GLN Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 225 ASN Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain D residue 738 LEU 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 937 LEU 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 1127 LEU Chi-restraints excluded: chain D residue 1142 LEU Chi-restraints excluded: chain D residue 1184 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 182 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 204 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3623 r_free = 0.3623 target = 0.127974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.100631 restraints weight = 26334.690| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.84 r_work: 0.3068 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17179 Z= 0.169 Angle : 0.529 13.872 23446 Z= 0.272 Chirality : 0.042 0.523 2909 Planarity : 0.004 0.049 2996 Dihedral : 3.527 16.831 2515 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.25 % Allowed : 14.94 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.18), residues: 2358 helix: 2.25 (0.13), residues: 1573 sheet: -2.73 (0.60), residues: 65 loop : -0.89 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 242 TYR 0.023 0.002 TYR D 878 PHE 0.025 0.001 PHE C 402 TRP 0.012 0.001 TRP R 33 HIS 0.006 0.001 HIS D 707 Details of bonding type rmsd covalent geometry : bond 0.00401 (17168) covalent geometry : angle 0.52839 (23440) hydrogen bonds : bond 0.05209 ( 1094) hydrogen bonds : angle 3.63573 ( 3219) metal coordination : bond 0.00754 ( 11) metal coordination : angle 1.26935 ( 6) *********************** 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 384 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 349 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 44 GLU cc_start: 0.8103 (tp30) cc_final: 0.7646 (tp30) REVERT: C 124 GLU cc_start: 0.7964 (tp30) cc_final: 0.7649 (mm-30) REVERT: C 131 LYS cc_start: 0.8586 (tppp) cc_final: 0.8271 (tppp) REVERT: C 170 CYS cc_start: 0.8179 (m) cc_final: 0.7899 (m) REVERT: C 199 ARG cc_start: 0.8415 (mmm-85) cc_final: 0.8182 (mmm-85) REVERT: C 478 ASN cc_start: 0.8305 (p0) cc_final: 0.7907 (p0) REVERT: C 509 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8132 (mt0) REVERT: C 573 ARG cc_start: 0.7998 (mmp80) cc_final: 0.7573 (mmp80) REVERT: C 641 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8091 (mp10) REVERT: D 93 THR cc_start: 0.9046 (m) cc_final: 0.8840 (t) REVERT: D 177 LEU cc_start: 0.8529 (tt) cc_final: 0.8300 (tt) REVERT: D 185 THR cc_start: 0.8823 (p) cc_final: 0.8478 (t) REVERT: D 457 MET cc_start: 0.8356 (mmm) cc_final: 0.8009 (tpp) REVERT: D 496 ASP cc_start: 0.7788 (m-30) cc_final: 0.7464 (m-30) REVERT: D 738 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8359 (mp) REVERT: D 769 ASN cc_start: 0.7738 (t0) cc_final: 0.7312 (t0) REVERT: D 857 LEU cc_start: 0.8682 (tp) cc_final: 0.8363 (tt) REVERT: D 971 LYS cc_start: 0.8602 (mmmt) cc_final: 0.8344 (tttp) REVERT: D 1099 ARG cc_start: 0.8454 (mmm-85) cc_final: 0.8181 (mmt180) REVERT: D 1174 ARG cc_start: 0.7975 (mtm-85) cc_final: 0.7649 (mtt180) REVERT: D 1177 MET cc_start: 0.8064 (mmm) cc_final: 0.7783 (mmm) REVERT: D 1195 MET cc_start: 0.7511 (tpp) cc_final: 0.7076 (tpp) outliers start: 35 outliers final: 23 residues processed: 362 average time/residue: 0.1402 time to fit residues: 73.9325 Evaluate side-chains 371 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 345 time to evaluate : 0.514 ------------------------------------------------------------------------------- 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 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 95 MET Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 225 ASN Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 288 LYS Chi-restraints excluded: chain D residue 738 LEU Chi-restraints excluded: chain D residue 763 VAL 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 937 LEU 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 1089 MET Chi-restraints excluded: chain D residue 1127 LEU Chi-restraints excluded: chain D residue 1142 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 8.9990 chunk 227 optimal weight: 50.0000 chunk 190 optimal weight: 3.9990 chunk 124 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 18 optimal weight: 0.0170 chunk 235 optimal weight: 50.0000 chunk 120 optimal weight: 0.0770 chunk 122 optimal weight: 0.0370 overall best weight: 0.3254 ------------------------------------------------------------------------------- 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 151 GLN D1021 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.132057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.104956 restraints weight = 26589.779| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.88 r_work: 0.3127 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17179 Z= 0.099 Angle : 0.491 16.532 23446 Z= 0.248 Chirality : 0.038 0.486 2909 Planarity : 0.004 0.049 2996 Dihedral : 3.370 16.721 2515 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.67 % Allowed : 16.42 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.05 (0.18), residues: 2358 helix: 2.44 (0.13), residues: 1572 sheet: -2.67 (0.60), residues: 65 loop : -0.75 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 741 TYR 0.019 0.001 TYR D 878 PHE 0.015 0.001 PHE C 402 TRP 0.012 0.001 TRP R 33 HIS 0.003 0.001 HIS D 707 Details of bonding type rmsd covalent geometry : bond 0.00212 (17168) covalent geometry : angle 0.49091 (23440) hydrogen bonds : bond 0.03561 ( 1094) hydrogen bonds : angle 3.38509 ( 3219) metal coordination : bond 0.00178 ( 11) metal coordination : angle 0.99013 ( 6) *********************** 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 370 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 344 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 124 GLU cc_start: 0.7937 (tp30) cc_final: 0.7650 (mm-30) REVERT: C 131 LYS cc_start: 0.8580 (tppp) cc_final: 0.8266 (tppp) REVERT: C 146 ARG cc_start: 0.7677 (mtm110) cc_final: 0.7470 (mtm110) REVERT: C 478 ASN cc_start: 0.8222 (p0) cc_final: 0.7862 (p0) REVERT: C 509 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8161 (mt0) REVERT: C 573 ARG cc_start: 0.7899 (mmp80) cc_final: 0.7698 (mmp80) REVERT: C 641 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.8133 (mp10) REVERT: D 185 THR cc_start: 0.8812 (p) cc_final: 0.8461 (t) REVERT: D 290 VAL cc_start: 0.7960 (m) cc_final: 0.7706 (p) REVERT: D 457 MET cc_start: 0.8258 (mmm) cc_final: 0.7922 (tpp) REVERT: D 485 ASN cc_start: 0.7807 (p0) cc_final: 0.7561 (p0) REVERT: D 496 ASP cc_start: 0.7714 (m-30) cc_final: 0.7362 (m-30) REVERT: D 600 LEU cc_start: 0.8739 (pp) cc_final: 0.8492 (pp) REVERT: D 769 ASN cc_start: 0.7695 (t0) cc_final: 0.7249 (t0) REVERT: D 857 LEU cc_start: 0.8593 (tp) cc_final: 0.8279 (tt) REVERT: D 971 LYS cc_start: 0.8582 (mmmt) cc_final: 0.8352 (tttp) REVERT: D 1099 ARG cc_start: 0.8423 (mmm-85) cc_final: 0.8148 (mmt180) REVERT: D 1174 ARG cc_start: 0.7926 (mtm-85) cc_final: 0.7655 (mtt-85) REVERT: D 1177 MET cc_start: 0.8053 (mmm) cc_final: 0.7800 (mmm) outliers start: 26 outliers final: 14 residues processed: 357 average time/residue: 0.1465 time to fit residues: 75.9196 Evaluate side-chains 352 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 336 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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 620 TYR Chi-restraints excluded: chain C residue 641 GLN Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 763 VAL 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 1142 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 157 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 192 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 236 optimal weight: 20.0000 chunk 230 optimal weight: 50.0000 chunk 104 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 272 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 = 0.3625 r_free = 0.3625 target = 0.128236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.101064 restraints weight = 26379.968| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.86 r_work: 0.3056 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17179 Z= 0.186 Angle : 0.550 15.065 23446 Z= 0.280 Chirality : 0.042 0.493 2909 Planarity : 0.004 0.048 2996 Dihedral : 3.476 16.860 2515 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.22 % Allowed : 17.00 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.18), residues: 2358 helix: 2.26 (0.13), residues: 1584 sheet: -2.72 (0.59), residues: 65 loop : -0.91 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 242 TYR 0.022 0.002 TYR D 878 PHE 0.027 0.001 PHE C 402 TRP 0.009 0.001 TRP R 33 HIS 0.005 0.001 HIS D 707 Details of bonding type rmsd covalent geometry : bond 0.00446 (17168) covalent geometry : angle 0.54997 (23440) hydrogen bonds : bond 0.05402 ( 1094) hydrogen bonds : angle 3.61864 ( 3219) metal coordination : bond 0.00896 ( 11) metal coordination : angle 1.32603 ( 6) *********************** 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 370 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 351 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 124 GLU cc_start: 0.7950 (tp30) cc_final: 0.7640 (mm-30) REVERT: C 131 LYS cc_start: 0.8589 (tppp) cc_final: 0.8248 (tppp) REVERT: C 478 ASN cc_start: 0.8322 (p0) cc_final: 0.7928 (p0) REVERT: C 509 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.8145 (mt0) REVERT: C 641 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8144 (mp10) REVERT: D 160 ASP cc_start: 0.8361 (t0) cc_final: 0.7994 (m-30) REVERT: D 181 LEU cc_start: 0.8991 (mm) cc_final: 0.8551 (mp) REVERT: D 185 THR cc_start: 0.8839 (p) cc_final: 0.8484 (t) REVERT: D 290 VAL cc_start: 0.8194 (m) cc_final: 0.7957 (p) REVERT: D 457 MET cc_start: 0.8393 (mmm) cc_final: 0.8049 (tpp) REVERT: D 496 ASP cc_start: 0.7822 (m-30) cc_final: 0.7489 (m-30) REVERT: D 769 ASN cc_start: 0.7760 (t0) cc_final: 0.7344 (t0) REVERT: D 857 LEU cc_start: 0.8663 (tp) cc_final: 0.8353 (tt) REVERT: D 971 LYS cc_start: 0.8588 (mmmt) cc_final: 0.8288 (tttp) REVERT: D 1083 LYS cc_start: 0.8370 (mtpp) cc_final: 0.8093 (mtmt) REVERT: D 1099 ARG cc_start: 0.8482 (mmm-85) cc_final: 0.8213 (mmt180) REVERT: D 1177 MET cc_start: 0.8063 (mmm) cc_final: 0.7798 (mmm) REVERT: D 1195 MET cc_start: 0.7528 (tpp) cc_final: 0.7083 (tpp) outliers start: 19 outliers final: 15 residues processed: 360 average time/residue: 0.1383 time to fit residues: 72.4073 Evaluate side-chains 364 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 347 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 LEU 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 620 TYR 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 685 LEU Chi-restraints excluded: chain D residue 763 VAL 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 1142 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 202 optimal weight: 7.9990 chunk 228 optimal weight: 40.0000 chunk 160 optimal weight: 0.0040 chunk 43 optimal weight: 0.3980 chunk 58 optimal weight: 0.9990 chunk 233 optimal weight: 50.0000 chunk 146 optimal weight: 0.9990 chunk 223 optimal weight: 0.9990 chunk 113 optimal weight: 0.0570 chunk 132 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 overall best weight: 0.3310 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.131530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.104516 restraints weight = 26399.664| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.87 r_work: 0.3130 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17179 Z= 0.104 Angle : 0.513 16.387 23446 Z= 0.257 Chirality : 0.039 0.496 2909 Planarity : 0.004 0.049 2996 Dihedral : 3.353 16.735 2515 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.29 % Allowed : 17.26 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.00 (0.18), residues: 2358 helix: 2.41 (0.13), residues: 1583 sheet: -2.63 (0.62), residues: 60 loop : -0.86 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1129 TYR 0.022 0.001 TYR D 878 PHE 0.017 0.001 PHE C 402 TRP 0.013 0.001 TRP R 33 HIS 0.003 0.001 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00227 (17168) covalent geometry : angle 0.51299 (23440) hydrogen bonds : bond 0.03727 ( 1094) hydrogen bonds : angle 3.38455 ( 3219) metal coordination : bond 0.00191 ( 11) metal coordination : angle 1.01612 ( 6) ********************** 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 362 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 342 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 124 GLU cc_start: 0.7969 (tp30) cc_final: 0.7688 (mm-30) REVERT: C 131 LYS cc_start: 0.8598 (tppp) cc_final: 0.8277 (tppp) REVERT: C 478 ASN cc_start: 0.8220 (p0) cc_final: 0.7838 (p0) REVERT: C 509 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8139 (mt0) REVERT: C 641 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.8118 (mp10) REVERT: D 160 ASP cc_start: 0.8351 (t0) cc_final: 0.7970 (m-30) REVERT: D 185 THR cc_start: 0.8832 (p) cc_final: 0.8476 (t) REVERT: D 290 VAL cc_start: 0.8040 (m) cc_final: 0.7811 (p) REVERT: D 457 MET cc_start: 0.8249 (mmm) cc_final: 0.7913 (tpp) REVERT: D 485 ASN cc_start: 0.7773 (p0) cc_final: 0.7558 (p0) REVERT: D 496 ASP cc_start: 0.7716 (m-30) cc_final: 0.7368 (m-30) REVERT: D 769 ASN cc_start: 0.7711 (t0) cc_final: 0.7306 (t0) REVERT: D 857 LEU cc_start: 0.8595 (tp) cc_final: 0.8289 (tt) REVERT: D 971 LYS cc_start: 0.8584 (mmmt) cc_final: 0.8362 (tttp) REVERT: D 1083 LYS cc_start: 0.8277 (mtpp) cc_final: 0.7990 (mtpt) REVERT: D 1099 ARG cc_start: 0.8413 (mmm-85) cc_final: 0.8133 (mmt180) REVERT: D 1177 MET cc_start: 0.8024 (mmm) cc_final: 0.7775 (mmm) outliers start: 20 outliers final: 14 residues processed: 351 average time/residue: 0.1390 time to fit residues: 69.8454 Evaluate side-chains 353 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 337 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 536 SER Chi-restraints excluded: chain C residue 586 SER Chi-restraints excluded: chain C residue 620 TYR 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 763 VAL Chi-restraints excluded: chain D residue 882 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 1142 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 59 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 186 optimal weight: 3.9990 chunk 122 optimal weight: 0.0980 chunk 211 optimal weight: 3.9990 chunk 102 optimal weight: 0.0000 chunk 136 optimal weight: 0.9980 chunk 132 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 180 optimal weight: 0.7980 chunk 166 optimal weight: 3.9990 overall best weight: 0.4584 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.131467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.104470 restraints weight = 26365.138| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.87 r_work: 0.3128 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17179 Z= 0.107 Angle : 0.509 16.430 23446 Z= 0.255 Chirality : 0.039 0.523 2909 Planarity : 0.004 0.049 2996 Dihedral : 3.272 16.414 2515 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.22 % Allowed : 17.19 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.06 (0.18), residues: 2358 helix: 2.47 (0.13), residues: 1583 sheet: -2.64 (0.62), residues: 60 loop : -0.85 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 573 TYR 0.023 0.001 TYR D 878 PHE 0.019 0.001 PHE C 402 TRP 0.019 0.001 TRP C 144 HIS 0.004 0.001 HIS D1108 Details of bonding type rmsd covalent geometry : bond 0.00241 (17168) covalent geometry : angle 0.50878 (23440) hydrogen bonds : bond 0.03811 ( 1094) hydrogen bonds : angle 3.37098 ( 3219) metal coordination : bond 0.00187 ( 11) metal coordination : angle 1.04391 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5087.26 seconds wall clock time: 87 minutes 31.60 seconds (5251.60 seconds total)