Starting phenix.real_space_refine on Sun Aug 4 20:36:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wej_37477/08_2024/8wej_37477.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wej_37477/08_2024/8wej_37477.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wej_37477/08_2024/8wej_37477.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wej_37477/08_2024/8wej_37477.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wej_37477/08_2024/8wej_37477.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wej_37477/08_2024/8wej_37477.cif" } resolution = 2.79 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= 0.016 sd= 0.086 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 Fe 2 7.16 5 P 8 5.49 5 Mg 2 5.21 5 S 54 5.16 5 C 6905 2.51 5 N 1782 2.21 5 O 1906 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 10659 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1030 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 128} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4549 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 546} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 67 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 8} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1643 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 6, 'TRANS': 212} Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 12, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 82 Chain: "E" Number of atoms: 1328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1328 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 11, 'TRANS': 166} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 51 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 32 Chain: "H" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 935 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 113} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 103} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 13 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 216 Unusual residues: {' MG': 1, 'FDA': 1, 'HEM': 2, 'NAG': 2, 'NDP': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 7.25, per 1000 atoms: 0.68 Number of scatterers: 10659 At special positions: 0 Unit cell: (91.492, 107.94, 185.04, 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) Fe 2 26.01 S 54 16.00 P 8 15.00 Mg 2 11.99 O 1906 8.00 N 1782 7.00 C 6905 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 244 " - pdb=" SG CYS B 257 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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=2, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG B 603 " - " ASN B 132 " " NAG B 604 " - " ASN B 240 " " NAG F 1 " - " ASN B 149 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.77 Conformation dependent library (CDL) restraints added in 1.9 seconds 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2500 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 12 sheets defined 50.4% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 35 through 54 removed outlier: 4.021A pdb=" N GLY A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 78 removed outlier: 4.472A pdb=" N MET A 73 " --> pdb=" O GLY A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 86 Processing helix chain 'A' and resid 86 through 102 Proline residue: A 100 - end of helix Processing helix chain 'A' and resid 104 through 127 removed outlier: 4.207A pdb=" N LEU A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N GLY A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 33 removed outlier: 6.360A pdb=" N LEU B 10 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N SER B 11 " --> pdb=" O ASN B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 38 No H-bonds generated for 'chain 'B' and resid 36 through 38' Processing helix chain 'B' and resid 39 through 47 Processing helix chain 'B' and resid 48 through 68 Proline residue: B 56 - end of helix removed outlier: 4.528A pdb=" N LEU B 68 " --> pdb=" O CYS B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 83 Processing helix chain 'B' and resid 87 through 94 removed outlier: 3.682A pdb=" N ARG B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 131 Processing helix chain 'B' and resid 135 through 144 removed outlier: 3.884A pdb=" N LEU B 144 " --> pdb=" O ALA B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 173 removed outlier: 3.521A pdb=" N LEU B 167 " --> pdb=" O PRO B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 193 Processing helix chain 'B' and resid 194 through 201 Processing helix chain 'B' and resid 201 through 210 Processing helix chain 'B' and resid 211 through 221 Processing helix chain 'B' and resid 232 through 239 Processing helix chain 'B' and resid 240 through 245 Processing helix chain 'B' and resid 247 through 251 Processing helix chain 'B' and resid 268 through 293 removed outlier: 4.569A pdb=" N GLY B 275 " --> pdb=" O LYS B 271 " (cutoff:3.500A) Proline residue: B 276 - end of helix Processing helix chain 'B' and resid 359 through 369 Processing helix chain 'B' and resid 378 through 382 Processing helix chain 'B' and resid 393 through 398 Processing helix chain 'B' and resid 413 through 428 Processing helix chain 'B' and resid 447 through 453 removed outlier: 3.594A pdb=" N ALA B 450 " --> pdb=" O ASP B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 468 Processing helix chain 'B' and resid 470 through 472 No H-bonds generated for 'chain 'B' and resid 470 through 472' Processing helix chain 'B' and resid 484 through 494 Processing helix chain 'B' and resid 515 through 527 Processing helix chain 'B' and resid 539 through 554 Processing helix chain 'D' and resid 2 through 19 Processing helix chain 'D' and resid 21 through 31 Processing helix chain 'D' and resid 36 through 50 Processing helix chain 'D' and resid 52 through 67 removed outlier: 3.672A pdb=" N LYS D 58 " --> pdb=" O THR D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 84 Processing helix chain 'D' and resid 86 through 100 Processing helix chain 'D' and resid 120 through 133 Processing helix chain 'D' and resid 136 through 149 removed outlier: 3.533A pdb=" N ALA D 140 " --> pdb=" O GLU D 136 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER D 149 " --> pdb=" O ALA D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 156 Processing helix chain 'D' and resid 157 through 167 removed outlier: 3.624A pdb=" N LYS D 161 " --> pdb=" O SER D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 191 removed outlier: 3.568A pdb=" N ALA D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 25 Processing helix chain 'E' and resid 61 through 65 Processing helix chain 'E' and resid 67 through 71 Processing helix chain 'E' and resid 86 through 96 removed outlier: 3.906A pdb=" N PHE E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG E 94 " --> pdb=" O PHE E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 105 Processing helix chain 'E' and resid 122 through 132 Processing helix chain 'E' and resid 138 through 149 Processing helix chain 'E' and resid 164 through 178 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.529A pdb=" N THR H 91 " --> pdb=" O THR H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.877A pdb=" N ILE L 83 " --> pdb=" O GLN L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 229 through 231 Processing sheet with id=AA2, first strand: chain 'B' and resid 351 through 356 removed outlier: 3.736A pdb=" N THR B 307 " --> pdb=" O HIS B 303 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LYS B 313 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ILE B 297 " --> pdb=" O LYS B 313 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N THR B 298 " --> pdb=" O SER D 207 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER D 207 " --> pdb=" O THR B 298 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL B 300 " --> pdb=" O VAL D 205 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 338 through 341 removed outlier: 7.240A pdb=" N PHE B 326 " --> pdb=" O GLY B 389 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N GLY B 389 " --> pdb=" O PHE B 326 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LYS B 328 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N VAL B 387 " --> pdb=" O LYS B 328 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 510 through 511 removed outlier: 7.109A pdb=" N LEU B 510 " --> pdb=" O TYR B 476 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ILE B 478 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE B 439 " --> pdb=" O SER B 475 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ASN B 477 " --> pdb=" O ILE B 439 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N PHE B 441 " --> pdb=" O ASN B 477 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N TYR B 479 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N TRP B 443 " --> pdb=" O TYR B 479 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL B 403 " --> pdb=" O GLY B 533 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N PHE B 535 " --> pdb=" O VAL B 403 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N MET B 405 " --> pdb=" O PHE B 535 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N CYS B 537 " --> pdb=" O MET B 405 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL B 407 " --> pdb=" O CYS B 537 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 152 through 156 removed outlier: 5.957A pdb=" N GLY C 154 " --> pdb=" O MET E 45 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N MET E 45 " --> pdb=" O GLY C 154 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASN E 43 " --> pdb=" O ILE C 156 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP E 38 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLN E 2 " --> pdb=" O ASN E 52 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N GLY E 54 " --> pdb=" O GLN E 2 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE E 4 " --> pdb=" O GLY E 54 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N TRP E 56 " --> pdb=" O ILE E 4 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N CYS E 6 " --> pdb=" O TRP E 56 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N THR E 58 " --> pdb=" O CYS E 6 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL E 8 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS E 153 " --> pdb=" O ILE E 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 106 through 108 Processing sheet with id=AA7, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.654A pdb=" N LYS H 45 " --> pdb=" O PHE H 41 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 58 through 60 Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AB3, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.453A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) 556 hydrogen bonds defined for protein. 1563 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.60 Time building geometry restraints manager: 4.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 3900 1.38 - 1.55: 6929 1.55 - 1.72: 34 1.72 - 1.90: 77 1.90 - 2.07: 8 Bond restraints: 10948 Sorted by residual: bond pdb=" C10 FDA B 607 " pdb=" C4X FDA B 607 " ideal model delta sigma weight residual 1.354 1.484 -0.130 2.00e-02 2.50e+03 4.24e+01 bond pdb=" C ASP D 34 " pdb=" O ASP D 34 " ideal model delta sigma weight residual 1.235 1.207 0.028 4.70e-03 4.53e+04 3.61e+01 bond pdb=" O2B NDP B 606 " pdb=" P2B NDP B 606 " ideal model delta sigma weight residual 1.833 1.614 0.219 3.80e-02 6.93e+02 3.33e+01 bond pdb=" C7 FDA B 607 " pdb=" C8 FDA B 607 " ideal model delta sigma weight residual 1.398 1.494 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" C5X FDA B 607 " pdb=" C9A FDA B 607 " ideal model delta sigma weight residual 1.396 1.487 -0.091 2.00e-02 2.50e+03 2.09e+01 ... (remaining 10943 not shown) Histogram of bond angle deviations from ideal: 86.76 - 105.22: 200 105.22 - 123.67: 14303 123.67 - 142.13: 448 142.13 - 160.58: 0 160.58 - 179.04: 4 Bond angle restraints: 14955 Sorted by residual: angle pdb=" PA NDP B 606 " pdb=" O3 NDP B 606 " pdb=" PN NDP B 606 " ideal model delta sigma weight residual 107.74 122.27 -14.53 1.95e+00 2.62e-01 5.53e+01 angle pdb=" C5D NDP B 606 " pdb=" O5D NDP B 606 " pdb=" PN NDP B 606 " ideal model delta sigma weight residual 104.93 123.17 -18.24 2.66e+00 1.41e-01 4.71e+01 angle pdb=" C5B NDP B 606 " pdb=" O5B NDP B 606 " pdb=" PA NDP B 606 " ideal model delta sigma weight residual 103.84 115.17 -11.33 1.91e+00 2.73e-01 3.50e+01 angle pdb=" C2D NDP B 606 " pdb=" C1D NDP B 606 " pdb=" N1N NDP B 606 " ideal model delta sigma weight residual 109.56 118.11 -8.55 2.33e+00 1.84e-01 1.34e+01 angle pdb=" O1B GTP E 200 " pdb=" PB GTP E 200 " pdb=" O2B GTP E 200 " ideal model delta sigma weight residual 109.50 120.44 -10.94 3.00e+00 1.11e-01 1.33e+01 ... (remaining 14950 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.31: 6234 31.31 - 62.61: 151 62.61 - 93.92: 18 93.92 - 125.23: 6 125.23 - 156.54: 4 Dihedral angle restraints: 6413 sinusoidal: 2527 harmonic: 3886 Sorted by residual: dihedral pdb=" O3B GTP E 200 " pdb=" O3A GTP E 200 " pdb=" PB GTP E 200 " pdb=" PA GTP E 200 " ideal model delta sinusoidal sigma weight residual 291.08 134.54 156.54 1 2.00e+01 2.50e-03 4.60e+01 dihedral pdb=" C5' GTP E 200 " pdb=" O5' GTP E 200 " pdb=" PA GTP E 200 " pdb=" O3A GTP E 200 " ideal model delta sinusoidal sigma weight residual 69.27 -165.20 -125.53 1 2.00e+01 2.50e-03 3.79e+01 dihedral pdb=" C8 GTP E 200 " pdb=" C1' GTP E 200 " pdb=" N9 GTP E 200 " pdb=" O4' GTP E 200 " ideal model delta sinusoidal sigma weight residual 104.59 -10.58 115.18 1 2.00e+01 2.50e-03 3.42e+01 ... (remaining 6410 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1327 0.053 - 0.106: 306 0.106 - 0.159: 46 0.159 - 0.212: 3 0.212 - 0.265: 3 Chirality restraints: 1685 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 9.27e+00 chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.43 0.03 2.00e-02 2.50e+03 2.36e+00 chirality pdb=" C1D NDP B 606 " pdb=" C2D NDP B 606 " pdb=" N1N NDP B 606 " pdb=" O4D NDP B 606 " both_signs ideal model delta sigma weight residual False 2.60 2.34 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 1682 not shown) Planarity restraints: 1834 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 570 " -0.032 2.00e-02 2.50e+03 2.27e-02 9.01e+00 pdb=" CG PHE B 570 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE B 570 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE B 570 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE B 570 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 570 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE B 570 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 338 " -0.014 2.00e-02 2.50e+03 1.33e-02 2.67e+00 pdb=" CG HIS B 338 " 0.028 2.00e-02 2.50e+03 pdb=" ND1 HIS B 338 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 HIS B 338 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 HIS B 338 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS B 338 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET D 163 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.63e+00 pdb=" C MET D 163 " -0.028 2.00e-02 2.50e+03 pdb=" O MET D 163 " 0.011 2.00e-02 2.50e+03 pdb=" N GLU D 164 " 0.009 2.00e-02 2.50e+03 ... (remaining 1831 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 115 2.57 - 3.15: 9245 3.15 - 3.74: 18186 3.74 - 4.32: 25906 4.32 - 4.90: 42488 Nonbonded interactions: 95940 Sorted by model distance: nonbonded pdb=" O2B GTP E 200 " pdb="MG MG E 201 " model vdw 1.991 2.170 nonbonded pdb=" OG1 THR E 35 " pdb="MG MG E 201 " model vdw 2.005 2.170 nonbonded pdb=" O3G GTP E 200 " pdb="MG MG E 201 " model vdw 2.069 2.170 nonbonded pdb=" NE2 HIS B 209 " pdb="FE HEM B 602 " model vdw 2.101 3.080 nonbonded pdb=" NE2 HIS B 222 " pdb="FE HEM B 601 " model vdw 2.101 3.080 ... (remaining 95935 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 33.500 Find NCS groups from input model: 0.120 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:14.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 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 0.219 10948 Z= 0.469 Angle : 0.911 18.239 14955 Z= 0.436 Chirality : 0.047 0.265 1685 Planarity : 0.006 0.061 1831 Dihedral : 14.700 156.536 3904 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.33 % Allowed : 2.89 % Favored : 94.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: -0.11 (0.23), residues: 1322 helix: 1.04 (0.21), residues: 585 sheet: -1.03 (0.32), residues: 229 loop : -0.81 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 337 HIS 0.012 0.002 HIS B 338 PHE 0.047 0.002 PHE B 570 TYR 0.015 0.002 TYR L 50 ARG 0.009 0.001 ARG E 120 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 222 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 95 ASP cc_start: 0.7256 (m-30) cc_final: 0.7009 (m-30) REVERT: B 312 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7885 (pmm) REVERT: B 373 LYS cc_start: 0.7023 (OUTLIER) cc_final: 0.6258 (mptt) REVERT: B 548 LYS cc_start: 0.8002 (mtmm) cc_final: 0.7556 (mmpt) REVERT: D 27 ASP cc_start: 0.8091 (m-30) cc_final: 0.7808 (t0) REVERT: D 122 GLU cc_start: 0.6471 (mt-10) cc_final: 0.6169 (tm-30) REVERT: E 176 VAL cc_start: 0.7163 (OUTLIER) cc_final: 0.6949 (t) REVERT: L 91 VAL cc_start: 0.8557 (m) cc_final: 0.8331 (m) outliers start: 25 outliers final: 8 residues processed: 239 average time/residue: 1.1135 time to fit residues: 288.7026 Evaluate side-chains 171 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 160 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain E residue 148 GLU Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain H residue 81 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 1.9990 chunk 97 optimal weight: 0.0970 chunk 54 optimal weight: 0.2980 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 429 ASN B 466 GLN ** D 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN ** D 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10948 Z= 0.234 Angle : 0.655 15.211 14955 Z= 0.308 Chirality : 0.043 0.173 1685 Planarity : 0.004 0.036 1831 Dihedral : 12.115 171.233 1663 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.08 % Allowed : 10.26 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.21 (0.23), residues: 1322 helix: 1.25 (0.21), residues: 588 sheet: -0.80 (0.32), residues: 224 loop : -0.62 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 380 HIS 0.005 0.001 HIS B 495 PHE 0.026 0.002 PHE B 570 TYR 0.022 0.002 TYR B 201 ARG 0.007 0.001 ARG E 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 158 time to evaluate : 2.912 Fit side-chains revert: symmetry clash REVERT: B 208 THR cc_start: 0.8130 (p) cc_final: 0.7826 (t) REVERT: B 373 LYS cc_start: 0.7122 (OUTLIER) cc_final: 0.6349 (mptt) REVERT: B 548 LYS cc_start: 0.7964 (mtmm) cc_final: 0.7494 (mmpt) REVERT: D 21 ASP cc_start: 0.8091 (t0) cc_final: 0.7850 (t0) REVERT: E 65 ASP cc_start: 0.8045 (m-30) cc_final: 0.7742 (m-30) REVERT: E 171 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: H 49 MET cc_start: 0.8485 (mtp) cc_final: 0.8153 (ttm) outliers start: 33 outliers final: 11 residues processed: 178 average time/residue: 1.1959 time to fit residues: 230.4249 Evaluate side-chains 151 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 138 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain E residue 171 GLU Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 113 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 97 optimal weight: 0.4980 chunk 79 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 104 optimal weight: 0.0010 chunk 116 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 429 ASN B 466 GLN B 489 ASN ** D 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10948 Z= 0.245 Angle : 0.614 15.003 14955 Z= 0.292 Chirality : 0.042 0.141 1685 Planarity : 0.004 0.038 1831 Dihedral : 11.201 174.810 1651 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.54 % Allowed : 11.75 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.23 (0.23), residues: 1322 helix: 1.27 (0.21), residues: 591 sheet: -0.81 (0.32), residues: 236 loop : -0.62 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 380 HIS 0.006 0.001 HIS B 115 PHE 0.028 0.002 PHE B 570 TYR 0.016 0.001 TYR B 201 ARG 0.004 0.001 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 148 time to evaluate : 1.071 Fit side-chains revert: symmetry clash REVERT: A 132 THR cc_start: 0.8449 (m) cc_final: 0.8220 (m) REVERT: B 373 LYS cc_start: 0.7122 (OUTLIER) cc_final: 0.6354 (mptt) REVERT: B 548 LYS cc_start: 0.7983 (mtmm) cc_final: 0.7475 (mmpt) REVERT: D 21 ASP cc_start: 0.8075 (t0) cc_final: 0.7852 (t0) REVERT: D 79 MET cc_start: 0.7410 (mmm) cc_final: 0.7082 (mmm) REVERT: D 150 MET cc_start: 0.6141 (OUTLIER) cc_final: 0.5859 (pmm) REVERT: E 65 ASP cc_start: 0.8077 (m-30) cc_final: 0.7821 (m-30) REVERT: E 171 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6979 (mp0) outliers start: 38 outliers final: 16 residues processed: 172 average time/residue: 1.1986 time to fit residues: 222.8024 Evaluate side-chains 150 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 131 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 171 GLU Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 116 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 0.6980 chunk 88 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 chunk 117 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 429 ASN B 466 GLN ** B 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 ASN E 92 ASN H 44 ASN L 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10948 Z= 0.273 Angle : 0.615 15.398 14955 Z= 0.291 Chirality : 0.043 0.153 1685 Planarity : 0.004 0.044 1831 Dihedral : 10.821 179.645 1649 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.73 % Allowed : 13.71 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.18 (0.23), residues: 1322 helix: 1.18 (0.21), residues: 590 sheet: -0.83 (0.32), residues: 228 loop : -0.58 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 380 HIS 0.007 0.002 HIS B 115 PHE 0.031 0.002 PHE B 570 TYR 0.016 0.002 TYR B 201 ARG 0.007 0.001 ARG E 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 142 time to evaluate : 1.160 Fit side-chains revert: symmetry clash REVERT: A 132 THR cc_start: 0.8441 (m) cc_final: 0.8215 (m) REVERT: B 148 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7676 (tt0) REVERT: B 373 LYS cc_start: 0.7204 (OUTLIER) cc_final: 0.6412 (mptt) REVERT: B 548 LYS cc_start: 0.8001 (mtmm) cc_final: 0.7466 (mmpt) REVERT: B 568 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7113 (mp0) REVERT: D 21 ASP cc_start: 0.8125 (t0) cc_final: 0.7920 (t0) REVERT: E 65 ASP cc_start: 0.8115 (m-30) cc_final: 0.7780 (m-30) REVERT: H 5 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.7272 (mt0) REVERT: L 89 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8395 (pt0) outliers start: 40 outliers final: 18 residues processed: 171 average time/residue: 1.1976 time to fit residues: 221.6303 Evaluate side-chains 154 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 131 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain B residue 148 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 568 GLU Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 429 ASN B 466 GLN ** B 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN H 44 ASN L 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10948 Z= 0.296 Angle : 0.619 15.880 14955 Z= 0.292 Chirality : 0.042 0.158 1685 Planarity : 0.004 0.048 1831 Dihedral : 10.719 175.488 1648 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.01 % Allowed : 14.27 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.13 (0.23), residues: 1322 helix: 1.13 (0.21), residues: 591 sheet: -0.84 (0.32), residues: 229 loop : -0.59 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 36 HIS 0.007 0.001 HIS B 115 PHE 0.032 0.002 PHE B 570 TYR 0.016 0.002 TYR B 201 ARG 0.010 0.001 ARG E 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 143 time to evaluate : 1.126 Fit side-chains revert: symmetry clash REVERT: A 132 THR cc_start: 0.8427 (OUTLIER) cc_final: 0.8201 (m) REVERT: B 148 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7686 (tt0) REVERT: B 373 LYS cc_start: 0.7249 (OUTLIER) cc_final: 0.6446 (mptt) REVERT: B 548 LYS cc_start: 0.7981 (mtmm) cc_final: 0.7462 (mmpt) REVERT: D 150 MET cc_start: 0.5915 (pmm) cc_final: 0.5569 (pmm) REVERT: E 65 ASP cc_start: 0.8069 (m-30) cc_final: 0.7848 (m-30) REVERT: E 166 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7665 (tttm) REVERT: H 5 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.7279 (mt0) REVERT: H 49 MET cc_start: 0.8477 (mtp) cc_final: 0.8262 (ttm) REVERT: H 78 GLN cc_start: 0.8474 (pt0) cc_final: 0.8241 (pt0) REVERT: L 89 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8388 (pt0) outliers start: 43 outliers final: 22 residues processed: 170 average time/residue: 1.0607 time to fit residues: 196.4112 Evaluate side-chains 162 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 134 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 148 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 0.5980 chunk 112 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 73 optimal weight: 0.0170 chunk 30 optimal weight: 2.9990 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 429 ASN B 466 GLN ** B 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN H 44 ASN L 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10948 Z= 0.211 Angle : 0.589 15.569 14955 Z= 0.277 Chirality : 0.041 0.142 1685 Planarity : 0.004 0.054 1831 Dihedral : 10.600 170.408 1648 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.26 % Allowed : 15.58 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.17 (0.23), residues: 1322 helix: 1.20 (0.21), residues: 595 sheet: -0.82 (0.31), residues: 236 loop : -0.63 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 36 HIS 0.006 0.001 HIS B 115 PHE 0.028 0.001 PHE B 570 TYR 0.016 0.001 TYR B 201 ARG 0.014 0.001 ARG E 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 143 time to evaluate : 1.249 Fit side-chains revert: symmetry clash REVERT: A 132 THR cc_start: 0.8415 (m) cc_final: 0.8193 (m) REVERT: B 148 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7681 (tt0) REVERT: D 21 ASP cc_start: 0.8096 (t0) cc_final: 0.7861 (t0) REVERT: D 150 MET cc_start: 0.5911 (pmm) cc_final: 0.5643 (pmm) REVERT: E 65 ASP cc_start: 0.8043 (m-30) cc_final: 0.7821 (m-30) REVERT: H 5 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.7272 (mt0) REVERT: H 78 GLN cc_start: 0.8424 (pt0) cc_final: 0.8209 (pt0) outliers start: 35 outliers final: 17 residues processed: 168 average time/residue: 1.0527 time to fit residues: 193.7837 Evaluate side-chains 151 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 132 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 148 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 5 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 91 optimal weight: 0.2980 chunk 70 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 429 ASN B 466 GLN ** B 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN H 44 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10948 Z= 0.251 Angle : 0.605 15.641 14955 Z= 0.284 Chirality : 0.042 0.158 1685 Planarity : 0.004 0.049 1831 Dihedral : 10.418 165.133 1644 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.08 % Allowed : 15.49 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.18 (0.23), residues: 1322 helix: 1.19 (0.21), residues: 596 sheet: -0.80 (0.32), residues: 236 loop : -0.62 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 36 HIS 0.007 0.001 HIS B 115 PHE 0.030 0.002 PHE B 570 TYR 0.015 0.002 TYR B 201 ARG 0.006 0.000 ARG D 181 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 142 time to evaluate : 1.216 Fit side-chains revert: symmetry clash REVERT: B 148 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7705 (tt0) REVERT: B 568 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.6903 (mt-10) REVERT: D 21 ASP cc_start: 0.8113 (t0) cc_final: 0.7844 (t0) REVERT: D 150 MET cc_start: 0.5939 (pmm) cc_final: 0.5697 (pmm) REVERT: E 65 ASP cc_start: 0.8053 (m-30) cc_final: 0.7828 (m-30) REVERT: H 5 GLN cc_start: 0.7614 (OUTLIER) cc_final: 0.7285 (mt0) outliers start: 33 outliers final: 21 residues processed: 163 average time/residue: 1.0934 time to fit residues: 193.8572 Evaluate side-chains 158 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 134 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 148 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 568 GLU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 39 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 97 optimal weight: 0.0370 chunk 113 optimal weight: 0.6980 chunk 119 optimal weight: 0.7980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 429 ASN B 466 GLN ** B 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN H 44 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10948 Z= 0.252 Angle : 0.608 15.757 14955 Z= 0.286 Chirality : 0.042 0.155 1685 Planarity : 0.004 0.051 1831 Dihedral : 10.356 160.627 1644 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.26 % Allowed : 16.42 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.20 (0.23), residues: 1322 helix: 1.18 (0.21), residues: 596 sheet: -0.63 (0.32), residues: 231 loop : -0.67 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 36 HIS 0.007 0.001 HIS B 115 PHE 0.030 0.002 PHE B 570 TYR 0.015 0.002 TYR B 201 ARG 0.005 0.001 ARG D 181 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 138 time to evaluate : 1.192 Fit side-chains revert: symmetry clash REVERT: A 104 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8090 (mp) REVERT: B 148 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7698 (tt0) REVERT: B 548 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7452 (mmpt) REVERT: B 568 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.6897 (mt-10) REVERT: D 21 ASP cc_start: 0.8106 (t0) cc_final: 0.7845 (t0) REVERT: D 81 TYR cc_start: 0.7525 (m-80) cc_final: 0.7320 (m-80) REVERT: E 65 ASP cc_start: 0.8050 (m-30) cc_final: 0.7807 (m-30) outliers start: 35 outliers final: 20 residues processed: 163 average time/residue: 1.2465 time to fit residues: 221.9165 Evaluate side-chains 156 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 132 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain B residue 148 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 548 LYS Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 568 GLU Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 195 LYS Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 39 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 69 optimal weight: 0.0670 chunk 50 optimal weight: 0.6980 chunk 90 optimal weight: 0.0770 chunk 35 optimal weight: 0.5980 chunk 104 optimal weight: 0.0030 chunk 109 optimal weight: 7.9990 chunk 76 optimal weight: 0.6980 chunk 122 optimal weight: 0.5980 overall best weight: 0.2686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 429 ASN B 466 GLN ** B 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 ASN ** D 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN ** E 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN ** H 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10948 Z= 0.178 Angle : 0.582 15.294 14955 Z= 0.275 Chirality : 0.041 0.186 1685 Planarity : 0.004 0.048 1831 Dihedral : 10.224 155.434 1644 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.33 % Allowed : 18.00 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.27 (0.23), residues: 1322 helix: 1.24 (0.21), residues: 599 sheet: -0.58 (0.32), residues: 231 loop : -0.66 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 36 HIS 0.005 0.001 HIS B 115 PHE 0.024 0.001 PHE B 570 TYR 0.014 0.001 TYR B 201 ARG 0.005 0.000 ARG D 181 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 135 time to evaluate : 1.296 Fit side-chains revert: symmetry clash REVERT: B 148 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7702 (tt0) REVERT: D 21 ASP cc_start: 0.8100 (t0) cc_final: 0.7863 (t0) REVERT: E 65 ASP cc_start: 0.8014 (m-30) cc_final: 0.7768 (m-30) outliers start: 25 outliers final: 17 residues processed: 154 average time/residue: 1.1655 time to fit residues: 195.4167 Evaluate side-chains 151 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 133 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain B residue 148 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 85 optimal weight: 6.9990 chunk 128 optimal weight: 0.5980 chunk 118 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 10 optimal weight: 0.0050 chunk 79 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 429 ASN ** B 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 ASN ** D 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN H 16 GLN ** H 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10948 Z= 0.247 Angle : 0.612 15.151 14955 Z= 0.288 Chirality : 0.042 0.179 1685 Planarity : 0.004 0.049 1831 Dihedral : 10.207 153.209 1644 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.15 % Allowed : 18.10 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.24 (0.23), residues: 1322 helix: 1.19 (0.21), residues: 595 sheet: -0.56 (0.33), residues: 230 loop : -0.65 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 36 HIS 0.007 0.001 HIS B 115 PHE 0.028 0.002 PHE B 570 TYR 0.020 0.002 TYR B 201 ARG 0.008 0.001 ARG B 199 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 135 time to evaluate : 1.326 Fit side-chains revert: symmetry clash REVERT: B 148 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7728 (tt0) REVERT: B 548 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7456 (mmpt) REVERT: D 21 ASP cc_start: 0.8069 (t0) cc_final: 0.7825 (t0) REVERT: D 184 ARG cc_start: 0.8248 (mmm-85) cc_final: 0.7849 (mpt90) REVERT: E 65 ASP cc_start: 0.8041 (m-30) cc_final: 0.7786 (m-30) outliers start: 23 outliers final: 15 residues processed: 149 average time/residue: 1.0747 time to fit residues: 174.6092 Evaluate side-chains 152 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 135 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 148 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 548 LYS Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 0.9980 chunk 94 optimal weight: 0.2980 chunk 15 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 89 optimal weight: 0.3980 chunk 5 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 ASN ** D 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN ** E 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 ASN E 92 ASN ** H 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.134061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.109241 restraints weight = 15432.023| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.81 r_work: 0.3371 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10948 Z= 0.215 Angle : 0.600 15.197 14955 Z= 0.282 Chirality : 0.042 0.163 1685 Planarity : 0.004 0.048 1831 Dihedral : 10.174 150.409 1644 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.77 % Allowed : 18.75 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.24 (0.23), residues: 1322 helix: 1.17 (0.21), residues: 602 sheet: -0.59 (0.33), residues: 231 loop : -0.62 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 36 HIS 0.006 0.001 HIS B 115 PHE 0.026 0.001 PHE B 570 TYR 0.021 0.001 TYR B 201 ARG 0.006 0.000 ARG D 181 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4271.28 seconds wall clock time: 75 minutes 42.13 seconds (4542.13 seconds total)