Starting phenix.real_space_refine on Tue Nov 14 22:00:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p39_17385/11_2023/8p39_17385_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p39_17385/11_2023/8p39_17385.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p39_17385/11_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_17385/11_2023/8p39_17385_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p39_17385/11_2023/8p39_17385_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p39_17385/11_2023/8p39_17385.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p39_17385/11_2023/8p39_17385.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p39_17385/11_2023/8p39_17385_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p39_17385/11_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-1.21rc1-5144/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: 4.96, per 1000 atoms: 0.51 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: 4.04 Conformation dependent library (CDL) restraints added in 1.8 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: 2.11 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: 2.57 Time building geometry restraints manager: 4.36 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: 5721 25.84 - 51.68: 163 51.68 - 77.53: 23 77.53 - 103.37: 4 103.37 - 129.21: 1 Dihedral angle restraints: 5912 sinusoidal: 2421 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 5909 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: 2.080 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: 8.840 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 30.450 Find NCS groups from input model: 0.260 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: 0.010 Load rotamer database and sin/cos tables:12.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.800 ------------------------------------------------------------------------------- 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 : 12.118 129.212 3674 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 : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 11 residues processed: 196 average time/residue: 1.1133 time to fit residues: 235.8087 Evaluate side-chains 141 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 130 time to evaluate : 1.029 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 0.2324 time to fit residues: 2.1565 ------------------------------------------------------------------------------- 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: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9920 Z= 0.259 Angle : 0.615 7.184 13424 Z= 0.320 Chirality : 0.045 0.157 1432 Planarity : 0.005 0.054 1738 Dihedral : 7.062 119.602 1335 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.87 % Favored : 92.80 % Rotamer: Outliers : 4.17 % Allowed : 14.44 % Favored : 81.40 % 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: 0.34 (0.23), residues: 494 sheet: 0.15 (0.49), residues: 127 loop : -2.17 (0.24), residues: 573 *********************** 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: 43 poor density : 137 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 22 residues processed: 166 average time/residue: 1.0707 time to fit residues: 192.8198 Evaluate side-chains 152 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 130 time to evaluate : 1.056 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 16 residues processed: 6 average time/residue: 0.5548 time to fit residues: 5.4257 ------------------------------------------------------------------------------- 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: 0.0970 chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 73 optimal weight: 0.0170 chunk 29 optimal weight: 0.2980 chunk 108 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 96 optimal weight: 0.0980 chunk 107 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 86 optimal weight: 0.4980 overall best weight: 0.2016 ------------------------------------------------------------------------------- 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 ** B 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6143 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9920 Z= 0.138 Angle : 0.531 6.788 13424 Z= 0.274 Chirality : 0.042 0.150 1432 Planarity : 0.003 0.043 1738 Dihedral : 6.648 116.320 1335 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.28 % Favored : 94.39 % Rotamer: Outliers : 3.97 % Allowed : 16.18 % Favored : 79.84 % 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: -1.13 (0.24), residues: 1194 helix: 0.55 (0.23), residues: 499 sheet: 0.06 (0.48), residues: 126 loop : -2.21 (0.24), residues: 569 *********************** 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 179 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 138 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 23 residues processed: 168 average time/residue: 1.2247 time to fit residues: 221.5927 Evaluate side-chains 157 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 134 time to evaluate : 1.031 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 20 residues processed: 5 average time/residue: 0.4603 time to fit residues: 4.3379 ------------------------------------------------------------------------------- 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: 0.0370 chunk 81 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 72 optimal weight: 0.0370 chunk 108 optimal weight: 0.6980 chunk 115 optimal weight: 7.9990 chunk 102 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 95 optimal weight: 0.0030 overall best weight: 0.2746 ------------------------------------------------------------------------------- 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: 0.6143 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9920 Z= 0.148 Angle : 0.527 7.042 13424 Z= 0.270 Chirality : 0.042 0.187 1432 Planarity : 0.004 0.043 1738 Dihedral : 6.454 115.254 1335 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.03 % Favored : 93.63 % Rotamer: Outliers : 3.97 % Allowed : 17.34 % Favored : 78.68 % 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: 0.64 (0.23), residues: 501 sheet: 0.01 (0.48), residues: 126 loop : -2.15 (0.24), residues: 567 *********************** 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 179 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 138 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 22 residues processed: 169 average time/residue: 1.1951 time to fit residues: 218.0756 Evaluate side-chains 154 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 132 time to evaluate : 1.059 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 19 residues processed: 3 average time/residue: 0.2154 time to fit residues: 2.3507 ------------------------------------------------------------------------------- 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: 0.9990 chunk 1 optimal weight: 0.9980 chunk 85 optimal weight: 0.0870 chunk 47 optimal weight: 0.0000 chunk 98 optimal weight: 0.6980 chunk 79 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 38 optimal weight: 0.0970 overall best weight: 0.2560 ------------------------------------------------------------------------------- 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: 0.6128 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9920 Z= 0.144 Angle : 0.517 6.446 13424 Z= 0.268 Chirality : 0.042 0.155 1432 Planarity : 0.003 0.042 1738 Dihedral : 6.355 117.876 1335 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.86 % Favored : 93.89 % Rotamer: Outliers : 3.97 % Allowed : 18.80 % Favored : 77.23 % 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: 0.69 (0.24), residues: 500 sheet: -0.06 (0.47), residues: 126 loop : -2.12 (0.24), residues: 568 *********************** 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 176 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 135 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 24 residues processed: 162 average time/residue: 1.1606 time to fit residues: 203.6662 Evaluate side-chains 157 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 133 time to evaluate : 1.037 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 21 residues processed: 4 average time/residue: 0.4363 time to fit residues: 3.6358 ------------------------------------------------------------------------------- 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: 1.9990 chunk 22 optimal weight: 0.0370 chunk 67 optimal weight: 0.9990 chunk 28 optimal weight: 0.0000 chunk 115 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 chunk 53 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 0.4980 chunk 111 optimal weight: 0.9990 overall best weight: 0.3262 ------------------------------------------------------------------------------- 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 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 GLN B 572 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6145 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9920 Z= 0.163 Angle : 0.532 6.791 13424 Z= 0.276 Chirality : 0.042 0.221 1432 Planarity : 0.003 0.043 1738 Dihedral : 6.175 114.007 1335 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.37 % Favored : 93.38 % Rotamer: Outliers : 4.26 % Allowed : 18.99 % 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: -0.96 (0.24), residues: 1194 helix: 0.65 (0.24), residues: 504 sheet: -0.11 (0.47), residues: 126 loop : -2.03 (0.25), residues: 564 *********************** 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 177 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 133 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 26 residues processed: 162 average time/residue: 1.1565 time to fit residues: 202.6189 Evaluate side-chains 160 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 134 time to evaluate : 0.927 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 22 residues processed: 4 average time/residue: 0.6300 time to fit residues: 4.3920 ------------------------------------------------------------------------------- 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: 0.0270 chunk 65 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 chunk 96 optimal weight: 0.2980 chunk 64 optimal weight: 0.5980 chunk 114 optimal weight: 0.2980 chunk 71 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 70 optimal weight: 0.0050 chunk 45 optimal weight: 0.9980 overall best weight: 0.2452 ------------------------------------------------------------------------------- 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 572 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6123 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9920 Z= 0.150 Angle : 0.552 9.328 13424 Z= 0.281 Chirality : 0.042 0.210 1432 Planarity : 0.003 0.042 1738 Dihedral : 5.997 111.956 1335 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.28 % Favored : 93.47 % Rotamer: Outliers : 3.68 % Allowed : 20.06 % 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: -0.93 (0.24), residues: 1194 helix: 0.65 (0.24), residues: 508 sheet: -0.13 (0.47), residues: 126 loop : -2.00 (0.25), residues: 560 *********************** 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 170 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 132 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 25 residues processed: 160 average time/residue: 1.1148 time to fit residues: 193.2368 Evaluate side-chains 153 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 128 time to evaluate : 0.992 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 22 residues processed: 3 average time/residue: 0.5661 time to fit residues: 3.5755 ------------------------------------------------------------------------------- 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: 2.9990 chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 90 optimal weight: 0.5980 chunk 104 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 572 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6238 moved from start: 0.2617 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= 0.282 Angle : 0.648 7.964 13424 Z= 0.336 Chirality : 0.046 0.230 1432 Planarity : 0.004 0.043 1738 Dihedral : 6.358 112.781 1335 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.20 % Favored : 92.55 % Rotamer: Outliers : 3.68 % Allowed : 19.67 % 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: -1.21 (0.24), residues: 1194 helix: 0.38 (0.23), residues: 508 sheet: -0.15 (0.47), residues: 127 loop : -2.14 (0.25), residues: 559 *********************** 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 174 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 136 time to evaluate : 1.094 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 25 residues processed: 163 average time/residue: 1.1480 time to fit residues: 202.9260 Evaluate side-chains 158 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 133 time to evaluate : 1.064 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 20 residues processed: 5 average time/residue: 0.7635 time to fit residues: 5.9143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.9958 > 50: distance: 70 - 76: 34.188 distance: 76 - 77: 41.158 distance: 77 - 80: 39.034 distance: 80 - 81: 39.440 distance: 82 - 83: 40.092 distance: 85 - 86: 54.908 distance: 87 - 88: 22.595 distance: 87 - 97: 38.947 distance: 89 - 90: 38.945 distance: 90 - 91: 35.193 distance: 90 - 92: 57.760 distance: 92 - 94: 38.761 distance: 93 - 95: 39.334 distance: 94 - 95: 40.989 distance: 97 - 98: 40.463 distance: 98 - 101: 39.935 distance: 99 - 100: 39.002 distance: 99 - 105: 15.848 distance: 102 - 103: 39.745 distance: 105 - 106: 37.916 distance: 106 - 107: 4.948 distance: 106 - 109: 54.518 distance: 107 - 108: 39.642 distance: 110 - 112: 4.754 distance: 111 - 113: 38.884 distance: 112 - 114: 35.970 distance: 112 - 115: 34.366 distance: 114 - 116: 29.455 distance: 115 - 117: 30.171 distance: 117 - 118: 51.245 distance: 119 - 120: 46.343 distance: 120 - 121: 18.758 distance: 120 - 123: 24.186 distance: 121 - 122: 56.816 distance: 123 - 124: 39.997 distance: 123 - 125: 32.624 distance: 126 - 127: 19.319 distance: 127 - 128: 20.639 distance: 128 - 130: 39.588 distance: 130 - 131: 39.854 distance: 131 - 132: 13.588 distance: 131 - 134: 30.408 distance: 132 - 133: 28.824 distance: 132 - 135: 41.249 distance: 135 - 136: 40.935 distance: 136 - 137: 14.813 distance: 137 - 138: 41.950 distance: 137 - 144: 46.541 distance: 139 - 140: 41.079 distance: 141 - 142: 40.787 distance: 144 - 145: 41.242 distance: 145 - 146: 40.141 distance: 145 - 148: 40.547 distance: 153 - 156: 39.413 distance: 154 - 160: 35.454 distance: 156 - 157: 40.426