Starting phenix.real_space_refine on Thu Mar 14 20:39:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p39_17385/03_2024/8p39_17385_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p39_17385/03_2024/8p39_17385.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p39_17385/03_2024/8p39_17385_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p39_17385/03_2024/8p39_17385_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p39_17385/03_2024/8p39_17385_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p39_17385/03_2024/8p39_17385.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p39_17385/03_2024/8p39_17385.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p39_17385/03_2024/8p39_17385_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p39_17385/03_2024/8p39_17385_updated.pdb" } resolution = 2.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 9 5.49 5 Mg 2 5.21 5 S 60 5.16 5 C 6087 2.51 5 N 1697 2.21 5 O 1849 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9705 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4435 Classifications: {'peptide': 552} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 531} Chain breaks: 1 Chain: "B" Number of atoms: 5174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 648, 5174 Classifications: {'peptide': 648} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 626} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'DGT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1, 'DGT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9172 SG CYS B 680 14.731 51.558 51.514 1.00 63.85 S ATOM 9194 SG CYS B 683 13.353 48.052 52.805 1.00 68.15 S ATOM 9285 SG CYS B 695 12.866 49.207 49.245 1.00 61.34 S ATOM 9307 SG CYS B 698 11.097 50.898 52.197 1.00 65.74 S Time building chain proxies: 5.52, per 1000 atoms: 0.57 Number of scatterers: 9705 At special positions: 0 Unit cell: (74.82, 104.06, 119.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 60 16.00 P 9 15.00 Mg 2 11.99 O 1849 8.00 N 1697 7.00 C 6087 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 - 3.50 Amino acid : False - 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: 3.76 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 804 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 698 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 695 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 683 " pdb="ZN ZN B 804 " - pdb=" SG CYS B 680 " Number of angles added : 6 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2238 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 7 sheets defined 42.5% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'A' and resid 122 through 139 removed outlier: 3.583A pdb=" N MET A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE A 129 " --> pdb=" O MET A 125 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A 130 " --> pdb=" O MET A 126 " (cutoff:3.500A) Proline residue: A 136 - end of helix removed outlier: 3.880A pdb=" N ASP A 139 " --> pdb=" O LYS A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 152 Processing helix chain 'A' and resid 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'A' and resid 176 through 182 removed outlier: 3.521A pdb=" N HIS A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 210 removed outlier: 3.591A pdb=" N CYS A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE A 206 " --> pdb=" O VAL A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 214 No H-bonds generated for 'chain 'A' and resid 212 through 214' Processing helix chain 'A' and resid 224 through 227 No H-bonds generated for 'chain 'A' and resid 224 through 227' Processing helix chain 'A' and resid 230 through 237 removed outlier: 3.634A pdb=" N TYR A 236 " --> pdb=" O VAL A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 242 No H-bonds generated for 'chain 'A' and resid 239 through 242' Processing helix chain 'A' and resid 273 through 301 removed outlier: 3.571A pdb=" N LEU A 276 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN A 278 " --> pdb=" O ARG A 275 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 280 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 281 " --> pdb=" O GLN A 278 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL A 285 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASN A 286 " --> pdb=" O LYS A 283 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 288 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET A 292 " --> pdb=" O HIS A 289 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE A 296 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN A 298 " --> pdb=" O PHE A 295 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N MET A 299 " --> pdb=" O ILE A 296 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR A 301 " --> pdb=" O ASN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 338 Processing helix chain 'A' and resid 368 through 381 removed outlier: 3.587A pdb=" N LEU A 373 " --> pdb=" O ASP A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 449 removed outlier: 3.677A pdb=" N ALA A 447 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE A 448 " --> pdb=" O VAL A 444 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU A 449 " --> pdb=" O LYS A 445 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 443 through 449' Processing helix chain 'A' and resid 456 through 487 removed outlier: 4.181A pdb=" N THR A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 513 through 515 No H-bonds generated for 'chain 'A' and resid 513 through 515' Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 545 through 569 Processing helix chain 'A' and resid 586 through 594 removed outlier: 3.633A pdb=" N LYS A 590 " --> pdb=" O LYS A 586 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN A 594 " --> pdb=" O LYS A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 634 Proline residue: A 630 - end of helix removed outlier: 4.341A pdb=" N ASP A 633 " --> pdb=" O ALA A 629 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU A 634 " --> pdb=" O PRO A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 665 removed outlier: 3.592A pdb=" N VAL A 659 " --> pdb=" O VAL A 655 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 660 " --> pdb=" O ILE A 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 103 removed outlier: 3.704A pdb=" N PHE B 99 " --> pdb=" O THR B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 141 Proline residue: B 136 - end of helix removed outlier: 3.565A pdb=" N ASP B 140 " --> pdb=" O PRO B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 152 removed outlier: 3.537A pdb=" N ALA B 150 " --> pdb=" O ASP B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 166 No H-bonds generated for 'chain 'B' and resid 164 through 166' Processing helix chain 'B' and resid 177 through 182 removed outlier: 3.590A pdb=" N HIS B 182 " --> pdb=" O VAL B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 214 removed outlier: 3.818A pdb=" N VAL B 202 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU B 203 " --> pdb=" O THR B 199 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N CYS B 205 " --> pdb=" O ALA B 201 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE B 206 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER B 207 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN B 213 " --> pdb=" O GLU B 209 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLU B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 227 No H-bonds generated for 'chain 'B' and resid 224 through 227' Processing helix chain 'B' and resid 229 through 247 removed outlier: 3.832A pdb=" N ARG B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 254 No H-bonds generated for 'chain 'B' and resid 252 through 254' Processing helix chain 'B' and resid 272 through 275 Processing helix chain 'B' and resid 278 through 297 removed outlier: 3.875A pdb=" N THR B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASN B 286 " --> pdb=" O ASN B 282 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG B 287 " --> pdb=" O LYS B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 304 Processing helix chain 'B' and resid 323 through 338 Processing helix chain 'B' and resid 366 through 378 removed outlier: 4.183A pdb=" N ASP B 369 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR B 378 " --> pdb=" O CYS B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 452 removed outlier: 3.540A pdb=" N CYS B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N GLY B 452 " --> pdb=" O ILE B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 486 Processing helix chain 'B' and resid 490 through 492 No H-bonds generated for 'chain 'B' and resid 490 through 492' Processing helix chain 'B' and resid 504 through 506 No H-bonds generated for 'chain 'B' and resid 504 through 506' Processing helix chain 'B' and resid 513 through 515 No H-bonds generated for 'chain 'B' and resid 513 through 515' Processing helix chain 'B' and resid 517 through 519 No H-bonds generated for 'chain 'B' and resid 517 through 519' Processing helix chain 'B' and resid 548 through 569 Processing helix chain 'B' and resid 587 through 594 Processing helix chain 'B' and resid 621 through 634 Proline residue: B 630 - end of helix removed outlier: 3.907A pdb=" N ASP B 633 " --> pdb=" O ALA B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 649 No H-bonds generated for 'chain 'B' and resid 647 through 649' Processing helix chain 'B' and resid 654 through 665 Processing helix chain 'B' and resid 717 through 719 No H-bonds generated for 'chain 'B' and resid 717 through 719' Processing helix chain 'B' and resid 722 through 730 removed outlier: 3.750A pdb=" N ASP B 730 " --> pdb=" O ALA B 726 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 156 through 158 removed outlier: 7.988A pdb=" N GLY A 523 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N PHE A 438 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N GLY A 525 " --> pdb=" O PHE A 438 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N THR A 440 " --> pdb=" O GLY A 525 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 576 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE A 526 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 172 through 174 removed outlier: 4.048A pdb=" N ALA A 220 " --> pdb=" O VAL A 172 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 314 through 317 removed outlier: 6.135A pdb=" N ILE A 350 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N TYR A 317 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ILE A 352 " --> pdb=" O TYR A 317 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASN A 385 " --> pdb=" O TRP A 353 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 641 through 644 Processing sheet with id= E, first strand: chain 'B' and resid 156 through 158 removed outlier: 7.711A pdb=" N THR B 521 " --> pdb=" O LEU B 436 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N PHE B 438 " --> pdb=" O THR B 521 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLY B 523 " --> pdb=" O PHE B 438 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N THR B 440 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N GLY B 525 " --> pdb=" O THR B 440 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ASN B 442 " --> pdb=" O GLY B 525 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ILE B 527 " --> pdb=" O ASN B 442 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 219 through 221 removed outlier: 6.223A pdb=" N ILE B 350 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N TYR B 317 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ILE B 352 " --> pdb=" O TYR B 317 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ASN B 385 " --> pdb=" O TRP B 353 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LYS B 355 " --> pdb=" O ASN B 385 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU B 387 " --> pdb=" O LYS B 355 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 641 through 644 287 hydrogen bonds defined for protein. 792 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 4.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3230 1.34 - 1.46: 1894 1.46 - 1.58: 4683 1.58 - 1.69: 15 1.69 - 1.81: 98 Bond restraints: 9920 Sorted by residual: bond pdb=" C2' DGT B 802 " pdb=" C3' DGT B 802 " ideal model delta sigma weight residual 1.284 1.525 -0.241 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C2' DGT A 801 " pdb=" C3' DGT A 801 " ideal model delta sigma weight residual 1.284 1.523 -0.239 2.00e-02 2.50e+03 1.43e+02 bond pdb=" C4' DGT A 801 " pdb=" O4' DGT A 801 " ideal model delta sigma weight residual 1.272 1.445 -0.173 2.00e-02 2.50e+03 7.44e+01 bond pdb=" C4' DGT B 802 " pdb=" O4' DGT B 802 " ideal model delta sigma weight residual 1.272 1.445 -0.173 2.00e-02 2.50e+03 7.44e+01 bond pdb=" C4 DGT A 801 " pdb=" N3 DGT A 801 " ideal model delta sigma weight residual 1.502 1.354 0.148 2.00e-02 2.50e+03 5.44e+01 ... (remaining 9915 not shown) Histogram of bond angle deviations from ideal: 99.76 - 107.78: 400 107.78 - 115.79: 6010 115.79 - 123.80: 6766 123.80 - 131.81: 230 131.81 - 139.82: 18 Bond angle restraints: 13424 Sorted by residual: angle pdb=" PA DGT B 802 " pdb=" O3A DGT B 802 " pdb=" PB DGT B 802 " ideal model delta sigma weight residual 123.57 135.67 -12.10 3.00e+00 1.11e-01 1.63e+01 angle pdb=" O1B DGT A 801 " pdb=" PB DGT A 801 " pdb=" O2B DGT A 801 " ideal model delta sigma weight residual 109.48 119.60 -10.12 3.00e+00 1.11e-01 1.14e+01 angle pdb=" O1B DGT B 802 " pdb=" PB DGT B 802 " pdb=" O2B DGT B 802 " ideal model delta sigma weight residual 109.48 119.51 -10.03 3.00e+00 1.11e-01 1.12e+01 angle pdb=" PB DGT A 801 " pdb=" O3B DGT A 801 " pdb=" PG DGT A 801 " ideal model delta sigma weight residual 123.56 133.39 -9.83 3.00e+00 1.11e-01 1.07e+01 angle pdb=" PA DGT A 801 " pdb=" O3A DGT A 801 " pdb=" PB DGT A 801 " ideal model delta sigma weight residual 123.57 133.21 -9.64 3.00e+00 1.11e-01 1.03e+01 ... (remaining 13419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.84: 5732 25.84 - 51.68: 179 51.68 - 77.53: 25 77.53 - 103.37: 6 103.37 - 129.21: 1 Dihedral angle restraints: 5943 sinusoidal: 2452 harmonic: 3491 Sorted by residual: dihedral pdb=" O1B DGT B 802 " pdb=" O3B DGT B 802 " pdb=" PB DGT B 802 " pdb=" PG DGT B 802 " ideal model delta sinusoidal sigma weight residual 301.68 172.47 129.21 1 3.00e+01 1.11e-03 1.74e+01 dihedral pdb=" CA TYR B 499 " pdb=" C TYR B 499 " pdb=" N LEU B 500 " pdb=" CA LEU B 500 " ideal model delta harmonic sigma weight residual -180.00 -162.24 -17.76 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" N ARG B 677 " pdb=" CA ARG B 677 " pdb=" CB ARG B 677 " pdb=" CG ARG B 677 " ideal model delta sinusoidal sigma weight residual -60.00 -119.58 59.58 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 5940 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1291 0.066 - 0.131: 138 0.131 - 0.197: 1 0.197 - 0.262: 0 0.262 - 0.328: 2 Chirality restraints: 1432 Sorted by residual: chirality pdb=" C3' DGT B 802 " pdb=" C2' DGT B 802 " pdb=" C4' DGT B 802 " pdb=" O3' DGT B 802 " both_signs ideal model delta sigma weight residual False -2.42 -2.75 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" C3' DGT A 801 " pdb=" C2' DGT A 801 " pdb=" C4' DGT A 801 " pdb=" O3' DGT A 801 " both_signs ideal model delta sigma weight residual False -2.42 -2.75 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA VAL A 613 " pdb=" N VAL A 613 " pdb=" C VAL A 613 " pdb=" CB VAL A 613 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.70e-01 ... (remaining 1429 not shown) Planarity restraints: 1738 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 121 " 0.026 5.00e-02 4.00e+02 3.91e-02 2.44e+00 pdb=" N PRO A 122 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 122 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 122 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 174 " -0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO B 175 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 175 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 175 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 403 " -0.022 5.00e-02 4.00e+02 3.35e-02 1.79e+00 pdb=" N PRO B 404 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 404 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 404 " -0.019 5.00e-02 4.00e+02 ... (remaining 1735 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 85 2.54 - 3.13: 7498 3.13 - 3.72: 15128 3.72 - 4.31: 21104 4.31 - 4.90: 35034 Nonbonded interactions: 78849 Sorted by model distance: nonbonded pdb="MG MG A 802 " pdb=" O3G DGT B 802 " model vdw 1.951 2.170 nonbonded pdb=" NE2 GLN B 290 " pdb="MG MG B 801 " model vdw 2.031 2.250 nonbonded pdb=" ND2 ASN A 154 " pdb=" OD1 ASP A 591 " model vdw 2.205 2.520 nonbonded pdb=" O HIS A 157 " pdb=" OG SER A 439 " model vdw 2.233 2.440 nonbonded pdb=" O ARG B 112 " pdb=" NH1 ARG B 719 " model vdw 2.236 2.520 ... (remaining 78844 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.240 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: 8.770 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 29.420 Find NCS groups from input model: 0.230 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: 0.010 Load rotamer database and sin/cos tables:13.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6167 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 : 0.007 0.241 9920 Z= 0.543 Angle : 0.630 12.099 13424 Z= 0.294 Chirality : 0.042 0.328 1432 Planarity : 0.003 0.039 1738 Dihedral : 12.567 129.212 3705 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.61 % Favored : 94.05 % Rotamer: Outliers : 5.43 % Allowed : 7.27 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.24), residues: 1194 helix: 0.03 (0.23), residues: 493 sheet: 0.11 (0.49), residues: 127 loop : -1.99 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 399 HIS 0.003 0.001 HIS B 289 PHE 0.010 0.001 PHE A 224 TYR 0.011 0.001 TYR A 164 ARG 0.005 0.000 ARG B 719 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 153 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 THR cc_start: 0.8173 (OUTLIER) cc_final: 0.7972 (t) REVERT: A 587 PHE cc_start: 0.7269 (OUTLIER) cc_final: 0.6964 (m-10) REVERT: B 284 THR cc_start: 0.4707 (OUTLIER) cc_final: 0.3419 (p) REVERT: B 292 MET cc_start: 0.5948 (mmp) cc_final: 0.5673 (mmp) REVERT: B 329 MET cc_start: 0.5415 (mtm) cc_final: 0.5180 (mtm) REVERT: B 397 GLU cc_start: 0.7322 (pm20) cc_final: 0.7111 (pm20) REVERT: B 406 ARG cc_start: 0.4735 (OUTLIER) cc_final: 0.2457 (tpm170) REVERT: B 414 MET cc_start: 0.4114 (mtm) cc_final: 0.3869 (mtm) outliers start: 56 outliers final: 11 residues processed: 196 average time/residue: 1.0843 time to fit residues: 229.5122 Evaluate side-chains 145 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 130 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 407 TYR Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 587 PHE Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 406 ARG Chi-restraints excluded: chain B residue 532 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 545 GLU Chi-restraints excluded: chain B residue 650 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 0.0000 chunk 90 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 69 optimal weight: 0.3980 chunk 108 optimal weight: 0.8980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 GLN A 351 GLN A 367 ASN A 395 GLN A 626 GLN A 632 HIS ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN B 485 GLN B 541 HIS B 632 HIS B 675 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6209 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9920 Z= 0.207 Angle : 0.576 6.509 13424 Z= 0.300 Chirality : 0.043 0.156 1432 Planarity : 0.004 0.051 1738 Dihedral : 9.310 118.639 1395 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.45 % Favored : 93.22 % Rotamer: Outliers : 4.26 % Allowed : 13.76 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.24), residues: 1194 helix: 0.35 (0.23), residues: 508 sheet: 0.15 (0.49), residues: 127 loop : -2.10 (0.25), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 399 HIS 0.008 0.001 HIS B 157 PHE 0.018 0.002 PHE A 482 TYR 0.021 0.002 TYR A 642 ARG 0.012 0.001 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 136 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 670 TYR cc_start: 0.6945 (t80) cc_final: 0.6742 (t80) REVERT: B 284 THR cc_start: 0.4512 (OUTLIER) cc_final: 0.2942 (p) REVERT: B 329 MET cc_start: 0.5442 (mtm) cc_final: 0.5224 (mtm) REVERT: B 397 GLU cc_start: 0.7353 (pm20) cc_final: 0.7123 (pm20) REVERT: B 406 ARG cc_start: 0.4925 (OUTLIER) cc_final: 0.2855 (tpm170) REVERT: B 414 MET cc_start: 0.4300 (mtm) cc_final: 0.4090 (mtm) REVERT: B 507 LEU cc_start: 0.6671 (OUTLIER) cc_final: 0.6187 (pt) outliers start: 44 outliers final: 23 residues processed: 167 average time/residue: 1.1302 time to fit residues: 203.6651 Evaluate side-chains 153 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 127 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 407 TYR Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 612 HIS Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 308 ASN Chi-restraints excluded: chain B residue 406 ARG Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 532 CYS Chi-restraints excluded: chain B residue 545 GLU Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 734 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 0.0770 chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 96 optimal weight: 0.0570 chunk 107 optimal weight: 0.6980 chunk 36 optimal weight: 0.0270 chunk 86 optimal weight: 0.0570 overall best weight: 0.1832 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 ASN ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6129 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9920 Z= 0.134 Angle : 0.513 6.180 13424 Z= 0.264 Chirality : 0.041 0.147 1432 Planarity : 0.003 0.037 1738 Dihedral : 8.627 117.722 1391 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.61 % Favored : 94.05 % Rotamer: Outliers : 3.59 % Allowed : 15.79 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.24), residues: 1194 helix: 0.62 (0.23), residues: 497 sheet: 0.09 (0.48), residues: 126 loop : -2.09 (0.24), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 399 HIS 0.011 0.001 HIS B 174 PHE 0.022 0.001 PHE B 129 TYR 0.012 0.001 TYR B 685 ARG 0.007 0.000 ARG B 366 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 137 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6906 (pm20) REVERT: B 284 THR cc_start: 0.4438 (OUTLIER) cc_final: 0.2635 (p) REVERT: B 397 GLU cc_start: 0.7339 (pm20) cc_final: 0.7109 (pm20) REVERT: B 406 ARG cc_start: 0.4774 (OUTLIER) cc_final: 0.2861 (tpm170) REVERT: B 545 GLU cc_start: 0.3687 (OUTLIER) cc_final: 0.3231 (pm20) REVERT: B 592 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.5634 (ttm110) outliers start: 37 outliers final: 15 residues processed: 166 average time/residue: 1.1960 time to fit residues: 213.7591 Evaluate side-chains 153 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 133 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 612 HIS Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 406 ARG Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 532 CYS Chi-restraints excluded: chain B residue 545 GLU Chi-restraints excluded: chain B residue 592 ARG Chi-restraints excluded: chain B residue 650 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 72 optimal weight: 0.0060 chunk 108 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 GLN B 611 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6191 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9920 Z= 0.209 Angle : 0.569 7.750 13424 Z= 0.291 Chirality : 0.043 0.167 1432 Planarity : 0.004 0.037 1738 Dihedral : 8.630 118.496 1386 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.37 % Favored : 93.30 % Rotamer: Outliers : 4.75 % Allowed : 16.96 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.24), residues: 1194 helix: 0.53 (0.23), residues: 505 sheet: 0.02 (0.48), residues: 126 loop : -2.11 (0.24), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 353 HIS 0.011 0.001 HIS B 174 PHE 0.019 0.002 PHE B 129 TYR 0.015 0.001 TYR B 631 ARG 0.006 0.000 ARG B 366 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 134 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7140 (pm20) REVERT: A 462 MET cc_start: 0.5261 (OUTLIER) cc_final: 0.4407 (tmm) REVERT: B 129 PHE cc_start: 0.7166 (m-80) cc_final: 0.6729 (m-80) REVERT: B 132 GLU cc_start: 0.6385 (OUTLIER) cc_final: 0.5964 (mp0) REVERT: B 284 THR cc_start: 0.4496 (OUTLIER) cc_final: 0.2776 (p) REVERT: B 397 GLU cc_start: 0.7363 (pm20) cc_final: 0.7136 (pm20) REVERT: B 406 ARG cc_start: 0.4902 (OUTLIER) cc_final: 0.2956 (tpm170) REVERT: B 592 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.5689 (ttm110) outliers start: 49 outliers final: 23 residues processed: 170 average time/residue: 1.1234 time to fit residues: 205.7926 Evaluate side-chains 161 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 132 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 308 ASN Chi-restraints excluded: chain B residue 406 ARG Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 532 CYS Chi-restraints excluded: chain B residue 545 GLU Chi-restraints excluded: chain B residue 592 ARG Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 672 SER Chi-restraints excluded: chain B residue 734 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 29 optimal weight: 0.2980 chunk 38 optimal weight: 0.0030 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6207 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9920 Z= 0.212 Angle : 0.571 7.275 13424 Z= 0.294 Chirality : 0.044 0.215 1432 Planarity : 0.004 0.038 1738 Dihedral : 8.744 130.084 1386 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.95 % Favored : 92.80 % Rotamer: Outliers : 4.36 % Allowed : 18.80 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.24), residues: 1194 helix: 0.46 (0.23), residues: 505 sheet: -0.00 (0.48), residues: 127 loop : -2.17 (0.24), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 399 HIS 0.009 0.001 HIS B 174 PHE 0.021 0.002 PHE B 129 TYR 0.014 0.001 TYR B 231 ARG 0.008 0.000 ARG B 366 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 137 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7212 (pm20) REVERT: A 462 MET cc_start: 0.5309 (OUTLIER) cc_final: 0.4474 (tmm) REVERT: A 497 MET cc_start: 0.7351 (mmt) cc_final: 0.6910 (mmp) REVERT: B 132 GLU cc_start: 0.6351 (OUTLIER) cc_final: 0.5910 (mp0) REVERT: B 284 THR cc_start: 0.4479 (OUTLIER) cc_final: 0.3184 (p) REVERT: B 397 GLU cc_start: 0.7364 (pm20) cc_final: 0.7147 (pm20) REVERT: B 406 ARG cc_start: 0.4932 (OUTLIER) cc_final: 0.3200 (tpm170) REVERT: B 507 LEU cc_start: 0.6898 (OUTLIER) cc_final: 0.6454 (pt) REVERT: B 592 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.5702 (ttm110) outliers start: 45 outliers final: 22 residues processed: 166 average time/residue: 1.1477 time to fit residues: 204.8477 Evaluate side-chains 165 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 136 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 308 ASN Chi-restraints excluded: chain B residue 406 ARG Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 532 CYS Chi-restraints excluded: chain B residue 545 GLU Chi-restraints excluded: chain B residue 592 ARG Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 734 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 0.0870 chunk 22 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 chunk 95 optimal weight: 0.0980 chunk 53 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 60 optimal weight: 0.0000 chunk 111 optimal weight: 1.9990 overall best weight: 0.2762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 GLN B 541 HIS B 572 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6154 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9920 Z= 0.153 Angle : 0.539 6.995 13424 Z= 0.279 Chirality : 0.042 0.227 1432 Planarity : 0.003 0.035 1738 Dihedral : 8.343 127.851 1386 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.37 % Favored : 93.38 % Rotamer: Outliers : 4.17 % Allowed : 19.38 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.24), residues: 1194 helix: 0.63 (0.24), residues: 499 sheet: -0.02 (0.48), residues: 127 loop : -2.07 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 353 HIS 0.012 0.001 HIS B 541 PHE 0.027 0.002 PHE B 129 TYR 0.027 0.001 TYR B 685 ARG 0.008 0.000 ARG B 366 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 138 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7159 (pm20) REVERT: A 462 MET cc_start: 0.5313 (OUTLIER) cc_final: 0.4486 (tmm) REVERT: B 132 GLU cc_start: 0.6337 (OUTLIER) cc_final: 0.5929 (mp0) REVERT: B 284 THR cc_start: 0.4439 (OUTLIER) cc_final: 0.2368 (m) REVERT: B 397 GLU cc_start: 0.7354 (pm20) cc_final: 0.7106 (pm20) REVERT: B 406 ARG cc_start: 0.4733 (OUTLIER) cc_final: 0.3146 (tpm170) REVERT: B 507 LEU cc_start: 0.6862 (OUTLIER) cc_final: 0.6467 (pt) REVERT: B 592 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.5721 (ttm110) outliers start: 43 outliers final: 18 residues processed: 164 average time/residue: 1.1974 time to fit residues: 210.9372 Evaluate side-chains 159 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 134 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 308 ASN Chi-restraints excluded: chain B residue 406 ARG Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 532 CYS Chi-restraints excluded: chain B residue 545 GLU Chi-restraints excluded: chain B residue 592 ARG Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 722 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 0.2980 chunk 65 optimal weight: 0.6980 chunk 84 optimal weight: 0.3980 chunk 96 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 114 optimal weight: 0.7980 chunk 71 optimal weight: 0.0670 chunk 69 optimal weight: 0.0970 chunk 52 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 overall best weight: 0.2916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 541 HIS B 572 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6152 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9920 Z= 0.163 Angle : 0.554 8.148 13424 Z= 0.286 Chirality : 0.042 0.217 1432 Planarity : 0.003 0.035 1738 Dihedral : 8.179 126.056 1386 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.45 % Favored : 93.30 % Rotamer: Outliers : 3.88 % Allowed : 19.77 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.24), residues: 1194 helix: 0.67 (0.24), residues: 492 sheet: -0.07 (0.47), residues: 127 loop : -2.06 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 353 HIS 0.009 0.001 HIS B 541 PHE 0.014 0.001 PHE B 226 TYR 0.012 0.001 TYR B 231 ARG 0.004 0.000 ARG B 679 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 135 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.6209 (mtm) REVERT: A 422 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7150 (pm20) REVERT: A 462 MET cc_start: 0.5323 (OUTLIER) cc_final: 0.4477 (tmm) REVERT: B 129 PHE cc_start: 0.7029 (m-80) cc_final: 0.6762 (m-80) REVERT: B 132 GLU cc_start: 0.6370 (OUTLIER) cc_final: 0.5935 (mp0) REVERT: B 284 THR cc_start: 0.4439 (OUTLIER) cc_final: 0.2619 (p) REVERT: B 397 GLU cc_start: 0.7359 (pm20) cc_final: 0.7129 (pm20) REVERT: B 406 ARG cc_start: 0.4666 (OUTLIER) cc_final: 0.3006 (tpm170) REVERT: B 507 LEU cc_start: 0.6822 (OUTLIER) cc_final: 0.6427 (pt) REVERT: B 592 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.5733 (ttm110) outliers start: 40 outliers final: 15 residues processed: 160 average time/residue: 1.1892 time to fit residues: 204.1998 Evaluate side-chains 156 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 133 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 406 ARG Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 532 CYS Chi-restraints excluded: chain B residue 545 GLU Chi-restraints excluded: chain B residue 592 ARG Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 722 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 10 optimal weight: 0.4980 chunk 90 optimal weight: 0.5980 chunk 104 optimal weight: 0.9990 chunk 109 optimal weight: 0.2980 chunk 100 optimal weight: 0.4980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 541 HIS B 572 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6191 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9920 Z= 0.210 Angle : 0.600 8.466 13424 Z= 0.310 Chirality : 0.044 0.238 1432 Planarity : 0.004 0.036 1738 Dihedral : 8.274 122.897 1386 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.45 % Favored : 93.30 % Rotamer: Outliers : 4.36 % Allowed : 19.48 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.24), residues: 1194 helix: 0.50 (0.23), residues: 500 sheet: -0.09 (0.48), residues: 127 loop : -2.03 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 353 HIS 0.008 0.001 HIS B 541 PHE 0.016 0.002 PHE B 226 TYR 0.015 0.001 TYR B 231 ARG 0.004 0.000 ARG B 679 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 142 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 TYR cc_start: 0.3085 (OUTLIER) cc_final: 0.2107 (p90) REVERT: A 422 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7220 (pm20) REVERT: A 462 MET cc_start: 0.5330 (OUTLIER) cc_final: 0.4499 (tmm) REVERT: A 576 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8000 (tp) REVERT: B 132 GLU cc_start: 0.6392 (OUTLIER) cc_final: 0.5937 (mp0) REVERT: B 284 THR cc_start: 0.4446 (OUTLIER) cc_final: 0.2483 (m) REVERT: B 406 ARG cc_start: 0.4806 (OUTLIER) cc_final: 0.3116 (tpm170) REVERT: B 592 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.5781 (ttm110) outliers start: 45 outliers final: 22 residues processed: 171 average time/residue: 1.1553 time to fit residues: 212.7162 Evaluate side-chains 169 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 139 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 308 ASN Chi-restraints excluded: chain B residue 406 ARG Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 532 CYS Chi-restraints excluded: chain B residue 545 GLU Chi-restraints excluded: chain B residue 592 ARG Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 672 SER Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain B residue 734 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 0.0070 chunk 83 optimal weight: 0.0020 chunk 32 optimal weight: 1.9990 chunk 96 optimal weight: 0.0270 chunk 101 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.3264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 541 HIS B 572 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6161 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9920 Z= 0.179 Angle : 0.580 8.772 13424 Z= 0.299 Chirality : 0.043 0.217 1432 Planarity : 0.003 0.036 1738 Dihedral : 8.164 120.426 1386 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.53 % Favored : 93.22 % Rotamer: Outliers : 3.49 % Allowed : 19.96 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.24), residues: 1194 helix: 0.50 (0.23), residues: 499 sheet: -0.12 (0.48), residues: 127 loop : -2.00 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 353 HIS 0.007 0.001 HIS B 541 PHE 0.016 0.002 PHE B 421 TYR 0.012 0.001 TYR B 231 ARG 0.005 0.000 ARG B 679 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 136 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 TYR cc_start: 0.2902 (OUTLIER) cc_final: 0.1915 (p90) REVERT: A 362 LEU cc_start: 0.4986 (OUTLIER) cc_final: 0.4427 (mp) REVERT: A 422 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7123 (pm20) REVERT: A 462 MET cc_start: 0.5378 (OUTLIER) cc_final: 0.4578 (tmm) REVERT: A 576 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8002 (tp) REVERT: B 132 GLU cc_start: 0.6369 (OUTLIER) cc_final: 0.5922 (mp0) REVERT: B 284 THR cc_start: 0.4413 (OUTLIER) cc_final: 0.2398 (m) REVERT: B 406 ARG cc_start: 0.4693 (OUTLIER) cc_final: 0.2894 (tpm170) REVERT: B 592 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.5769 (ttm110) outliers start: 36 outliers final: 20 residues processed: 161 average time/residue: 1.1976 time to fit residues: 206.9183 Evaluate side-chains 163 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 134 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 406 ARG Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 532 CYS Chi-restraints excluded: chain B residue 545 GLU Chi-restraints excluded: chain B residue 592 ARG Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 672 SER Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain B residue 734 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 0.1980 chunk 78 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 94 optimal weight: 0.2980 chunk 9 optimal weight: 0.2980 chunk 72 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 28 optimal weight: 0.0870 overall best weight: 0.2958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 541 HIS B 572 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6149 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9920 Z= 0.170 Angle : 0.590 11.258 13424 Z= 0.303 Chirality : 0.043 0.206 1432 Planarity : 0.004 0.037 1738 Dihedral : 8.118 118.721 1386 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.11 % Favored : 93.63 % Rotamer: Outliers : 3.68 % Allowed : 20.25 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.24), residues: 1194 helix: 0.61 (0.24), residues: 487 sheet: -0.12 (0.48), residues: 127 loop : -2.03 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 353 HIS 0.008 0.001 HIS B 541 PHE 0.018 0.002 PHE B 226 TYR 0.020 0.001 TYR B 642 ARG 0.005 0.000 ARG B 679 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 134 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 TYR cc_start: 0.2838 (OUTLIER) cc_final: 0.1854 (p90) REVERT: A 422 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7105 (pm20) REVERT: A 462 MET cc_start: 0.5163 (OUTLIER) cc_final: 0.4455 (tmm) REVERT: A 576 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8016 (tp) REVERT: B 132 GLU cc_start: 0.6350 (OUTLIER) cc_final: 0.5904 (mp0) REVERT: B 284 THR cc_start: 0.4388 (OUTLIER) cc_final: 0.2336 (m) REVERT: B 406 ARG cc_start: 0.4645 (OUTLIER) cc_final: 0.2958 (tpm170) REVERT: B 507 LEU cc_start: 0.6930 (OUTLIER) cc_final: 0.6644 (pt) REVERT: B 592 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.5762 (ttm110) outliers start: 38 outliers final: 23 residues processed: 160 average time/residue: 1.1918 time to fit residues: 204.6568 Evaluate side-chains 163 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 131 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 439 SER Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 406 ARG Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 532 CYS Chi-restraints excluded: chain B residue 545 GLU Chi-restraints excluded: chain B residue 592 ARG Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 652 ASN Chi-restraints excluded: chain B residue 672 SER Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain B residue 734 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 94 optimal weight: 0.0670 chunk 39 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 541 HIS B 572 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.194545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.183266 restraints weight = 12505.822| |-----------------------------------------------------------------------------| r_work (start): 0.4427 rms_B_bonded: 1.57 r_work: 0.4351 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.4230 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.4230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6256 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9920 Z= 0.252 Angle : 0.653 9.754 13424 Z= 0.335 Chirality : 0.045 0.238 1432 Planarity : 0.004 0.036 1738 Dihedral : 8.472 117.407 1386 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.45 % Favored : 92.29 % Rotamer: Outliers : 3.88 % Allowed : 20.06 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.24), residues: 1194 helix: 0.37 (0.23), residues: 504 sheet: -0.14 (0.48), residues: 127 loop : -2.09 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 353 HIS 0.009 0.001 HIS B 174 PHE 0.022 0.002 PHE A 224 TYR 0.019 0.002 TYR B 642 ARG 0.005 0.000 ARG B 679 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4041.80 seconds wall clock time: 72 minutes 11.57 seconds (4331.57 seconds total)