Starting phenix.real_space_refine (version: 1.21rc1) on Wed Oct 4 23:28:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p39_17385/10_2023/8p39_17385_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p39_17385/10_2023/8p39_17385.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p39_17385/10_2023/8p39_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_17385/10_2023/8p39_17385_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p39_17385/10_2023/8p39_17385_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p39_17385/10_2023/8p39_17385.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p39_17385/10_2023/8p39_17385.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p39_17385/10_2023/8p39_17385_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p39_17385/10_2023/8p39_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-1.21rc1-5097/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: 5.31, per 1000 atoms: 0.55 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: 3.84 Conformation dependent library (CDL) restraints added in 1.4 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: 1.96 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: 2.63 Time building geometry restraints manager: 4.08 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: 5718 25.84 - 51.68: 161 51.68 - 77.53: 17 77.53 - 103.37: 3 103.37 - 129.21: 1 Dihedral angle restraints: 5900 sinusoidal: 2409 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 5897 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: 8.950 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 30.000 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.970 ------------------------------------------------------------------------------- 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 : 11.754 129.212 3662 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 *********************** 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 : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 11 residues processed: 196 average time/residue: 1.1704 time to fit residues: 247.4493 Evaluate side-chains 141 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 130 time to evaluate : 1.096 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 0.2279 time to fit residues: 2.0469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 0.9980 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: 0.5980 chunk 108 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 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 Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6241 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9920 Z= 0.265 Angle : 0.614 7.125 13424 Z= 0.320 Chirality : 0.045 0.157 1432 Planarity : 0.005 0.054 1738 Dihedral : 5.774 119.755 1323 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.78 % Favored : 92.88 % Rotamer: Outliers : 3.97 % Allowed : 14.53 % Favored : 81.49 % 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: -1.25 (0.24), residues: 1194 helix: 0.32 (0.23), residues: 500 sheet: 0.15 (0.49), residues: 127 loop : -2.19 (0.24), residues: 567 *********************** 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 178 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 137 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 23 residues processed: 164 average time/residue: 1.1356 time to fit residues: 201.4271 Evaluate side-chains 152 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 129 time to evaluate : 1.341 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 16 residues processed: 7 average time/residue: 0.5021 time to fit residues: 5.8959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 73 optimal weight: 0.0060 chunk 29 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 96 optimal weight: 0.0670 chunk 107 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 overall best weight: 0.4734 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6212 moved from start: 0.1912 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= 0.198 Angle : 0.576 7.578 13424 Z= 0.298 Chirality : 0.043 0.169 1432 Planarity : 0.004 0.047 1738 Dihedral : 5.728 118.646 1323 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.86 % Favored : 93.80 % Rotamer: Outliers : 4.94 % Allowed : 15.70 % Favored : 79.36 % 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: -1.26 (0.24), residues: 1194 helix: 0.33 (0.23), residues: 512 sheet: 0.03 (0.48), residues: 127 loop : -2.23 (0.24), residues: 555 *********************** 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 187 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 136 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 24 residues processed: 174 average time/residue: 1.1995 time to fit residues: 224.8418 Evaluate side-chains 156 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 132 time to evaluate : 0.916 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 19 residues processed: 5 average time/residue: 0.2060 time to fit residues: 3.1494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 11 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 72 optimal weight: 0.0270 chunk 108 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 102 optimal weight: 0.3980 chunk 30 optimal weight: 0.8980 chunk 95 optimal weight: 0.0470 overall best weight: 0.3736 ------------------------------------------------------------------------------- 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: 0.6184 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9920 Z= 0.175 Angle : 0.555 7.455 13424 Z= 0.287 Chirality : 0.043 0.184 1432 Planarity : 0.004 0.045 1738 Dihedral : 5.625 115.740 1323 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.28 % Favored : 93.38 % Rotamer: Outliers : 4.17 % Allowed : 16.96 % Favored : 78.88 % 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: -1.22 (0.24), residues: 1194 helix: 0.45 (0.23), residues: 503 sheet: -0.03 (0.48), residues: 127 loop : -2.24 (0.24), residues: 564 *********************** 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: 43 poor density : 140 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 21 residues processed: 167 average time/residue: 1.1862 time to fit residues: 213.9849 Evaluate side-chains 159 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 138 time to evaluate : 1.019 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 16 residues processed: 5 average time/residue: 0.3893 time to fit residues: 3.8923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 29 optimal weight: 0.0980 chunk 38 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.6225 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9920 Z= 0.230 Angle : 0.585 6.998 13424 Z= 0.303 Chirality : 0.044 0.157 1432 Planarity : 0.004 0.047 1738 Dihedral : 5.776 113.466 1323 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.29 % Favored : 92.46 % Rotamer: Outliers : 4.75 % Allowed : 18.31 % Favored : 76.94 % 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: -1.26 (0.24), residues: 1194 helix: 0.38 (0.23), residues: 508 sheet: -0.06 (0.48), residues: 127 loop : -2.25 (0.24), residues: 559 *********************** 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 192 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 143 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 28 residues processed: 173 average time/residue: 1.0779 time to fit residues: 202.2677 Evaluate side-chains 165 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 137 time to evaluate : 1.019 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 19 residues processed: 10 average time/residue: 0.4731 time to fit residues: 7.0872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 0.0770 chunk 22 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 28 optimal weight: 0.0370 chunk 115 optimal weight: 0.2980 chunk 95 optimal weight: 0.0030 chunk 53 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 overall best weight: 0.2026 ------------------------------------------------------------------------------- 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 541 HIS B 572 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6141 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9920 Z= 0.142 Angle : 0.530 6.555 13424 Z= 0.277 Chirality : 0.042 0.224 1432 Planarity : 0.003 0.046 1738 Dihedral : 5.474 110.073 1323 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.95 % Favored : 93.80 % Rotamer: Outliers : 3.88 % Allowed : 19.48 % Favored : 76.65 % 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: -1.05 (0.24), residues: 1194 helix: 0.65 (0.24), residues: 493 sheet: -0.02 (0.47), residues: 126 loop : -2.15 (0.24), residues: 575 *********************** 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 178 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 138 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 21 residues processed: 169 average time/residue: 1.1041 time to fit residues: 202.1777 Evaluate side-chains 156 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 135 time to evaluate : 1.047 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 20 residues processed: 3 average time/residue: 0.8437 time to fit residues: 4.3397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 0.3980 chunk 65 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 114 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 541 HIS B 572 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6219 moved from start: 0.2548 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= 0.232 Angle : 0.606 7.854 13424 Z= 0.315 Chirality : 0.044 0.239 1432 Planarity : 0.004 0.046 1738 Dihedral : 5.747 114.306 1323 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.37 % Favored : 92.38 % Rotamer: Outliers : 3.88 % Allowed : 19.38 % Favored : 76.74 % 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: 0.46 (0.23), residues: 501 sheet: -0.13 (0.48), residues: 127 loop : -2.11 (0.24), residues: 566 *********************** 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 178 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 138 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 24 residues processed: 163 average time/residue: 1.1960 time to fit residues: 210.7509 Evaluate side-chains 165 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 141 time to evaluate : 1.114 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 20 residues processed: 5 average time/residue: 0.3251 time to fit residues: 3.7069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 72 optimal weight: 0.3980 chunk 78 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 90 optimal weight: 0.4980 chunk 104 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 100 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 541 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6214 moved from start: 0.2624 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= 0.225 Angle : 0.626 8.648 13424 Z= 0.322 Chirality : 0.045 0.239 1432 Planarity : 0.004 0.048 1738 Dihedral : 5.745 111.903 1323 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.78 % Favored : 92.96 % Rotamer: Outliers : 3.39 % Allowed : 19.96 % Favored : 76.65 % 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: -1.24 (0.24), residues: 1194 helix: 0.39 (0.23), residues: 497 sheet: -0.10 (0.48), residues: 126 loop : -2.17 (0.24), residues: 571 *********************** 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 175 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 140 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 29 residues processed: 163 average time/residue: 1.1855 time to fit residues: 208.8074 Evaluate side-chains 167 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 138 time to evaluate : 1.032 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 23 residues processed: 8 average time/residue: 0.3891 time to fit residues: 5.1915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.2980 chunk 109 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 96 optimal weight: 0.0670 chunk 101 optimal weight: 0.9990 chunk 70 optimal weight: 0.1980 chunk 113 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.3918 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 541 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6185 moved from start: 0.2722 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= 0.190 Angle : 0.597 8.492 13424 Z= 0.308 Chirality : 0.043 0.224 1432 Planarity : 0.004 0.048 1738 Dihedral : 5.608 109.200 1323 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.28 % Favored : 93.47 % Rotamer: Outliers : 3.00 % Allowed : 20.64 % 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: -1.14 (0.24), residues: 1194 helix: 0.47 (0.23), residues: 499 sheet: -0.15 (0.48), residues: 127 loop : -2.09 (0.25), residues: 568 *********************** 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 170 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 139 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 26 residues processed: 162 average time/residue: 1.2616 time to fit residues: 219.7678 Evaluate side-chains 162 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 136 time to evaluate : 1.090 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 23 residues processed: 5 average time/residue: 0.3438 time to fit residues: 3.5568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 94 optimal weight: 0.3980 chunk 9 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 541 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6242 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9920 Z= 0.270 Angle : 0.667 10.498 13424 Z= 0.345 Chirality : 0.046 0.235 1432 Planarity : 0.004 0.048 1738 Dihedral : 5.819 109.511 1323 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.45 % Favored : 92.29 % Rotamer: Outliers : 2.71 % Allowed : 21.03 % Favored : 76.26 % 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: -1.32 (0.24), residues: 1194 helix: 0.30 (0.23), residues: 497 sheet: -0.12 (0.48), residues: 127 loop : -2.19 (0.25), residues: 570 ********************** 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 169 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 141 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 22 residues processed: 163 average time/residue: 1.1769 time to fit residues: 207.1718 Evaluate side-chains 161 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 139 time to evaluate : 1.025 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 20 residues processed: 3 average time/residue: 0.1547 time to fit residues: 2.2596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 0.1980 chunk 13 optimal weight: 0.4980 chunk 26 optimal weight: 0.4980 chunk 94 optimal weight: 0.1980 chunk 39 optimal weight: 0.0010 chunk 97 optimal weight: 2.9990 chunk 11 optimal weight: 0.0040 chunk 17 optimal weight: 1.9990 chunk 83 optimal weight: 0.0570 chunk 5 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 overall best weight: 0.0916 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.200092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.188714 restraints weight = 12572.992| |-----------------------------------------------------------------------------| r_work (start): 0.4480 rms_B_bonded: 1.61 r_work: 0.4405 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.4282 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.4282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6157 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 9920 Z= 0.150 Angle : 0.581 9.371 13424 Z= 0.298 Chirality : 0.042 0.184 1432 Planarity : 0.004 0.054 1738 Dihedral : 5.428 105.327 1323 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.78 % Favored : 93.97 % Rotamer: Outliers : 2.42 % Allowed : 21.12 % 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: -1.03 (0.24), residues: 1194 helix: 0.63 (0.24), residues: 490 sheet: 0.00 (0.49), residues: 126 loop : -2.09 (0.25), residues: 578 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4078.27 seconds wall clock time: 73 minutes 30.32 seconds (4410.32 seconds total)