Starting phenix.real_space_refine on Fri Mar 15 05:19:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wej_37477/03_2024/8wej_37477_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wej_37477/03_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_37477/03_2024/8wej_37477.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wej_37477/03_2024/8wej_37477.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wej_37477/03_2024/8wej_37477_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wej_37477/03_2024/8wej_37477_updated.pdb" } 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-5265/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: 6.49, per 1000 atoms: 0.61 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: 4.67 Conformation dependent library (CDL) restraints added in 2.1 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... running ksdssp... Secondary structure from input PDB file: 49 helices and 12 sheets defined 44.9% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'A' and resid 6 through 30 Processing helix chain 'A' and resid 36 through 54 Processing helix chain 'A' and resid 70 through 85 removed outlier: 3.627A pdb=" N LEU A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N PHE A 80 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLY A 81 " --> pdb=" O VAL A 77 " (cutoff:3.500A) Proline residue: A 82 - end of helix Processing helix chain 'A' and resid 87 through 103 Proline residue: A 100 - end of helix removed outlier: 4.459A pdb=" N PHE A 103 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 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 5 through 32 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 37 through 46 removed outlier: 5.419A pdb=" N TYR B 41 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU B 46 " --> pdb=" O ARG B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 67 Proline residue: B 56 - end of helix Processing helix chain 'B' and resid 73 through 82 Processing helix chain 'B' and resid 88 through 130 removed outlier: 3.544A pdb=" N ASP B 95 " --> pdb=" O ARG B 91 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG B 96 " --> pdb=" O ARG B 92 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ASN B 97 " --> pdb=" O GLN B 93 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU B 98 " --> pdb=" O LEU B 94 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N THR B 99 " --> pdb=" O ASP B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 143 Processing helix chain 'B' and resid 164 through 172 Processing helix chain 'B' and resid 174 through 192 Processing helix chain 'B' and resid 195 through 200 Processing helix chain 'B' and resid 202 through 220 removed outlier: 4.574A pdb=" N LEU B 211 " --> pdb=" O TYR B 207 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N PHE B 212 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N VAL B 213 " --> pdb=" O HIS B 209 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE B 214 " --> pdb=" O HIS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 238 Processing helix chain 'B' and resid 241 through 244 No H-bonds generated for 'chain 'B' and resid 241 through 244' Processing helix chain 'B' and resid 248 through 250 No H-bonds generated for 'chain 'B' and resid 248 through 250' Processing helix chain 'B' and resid 269 through 292 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 360 through 368 Processing helix chain 'B' and resid 379 through 381 No H-bonds generated for 'chain 'B' and resid 379 through 381' Processing helix chain 'B' and resid 394 through 397 Processing helix chain 'B' and resid 414 through 427 Processing helix chain 'B' and resid 448 through 453 Processing helix chain 'B' and resid 455 through 467 Processing helix chain 'B' and resid 471 through 473 No H-bonds generated for 'chain 'B' and resid 471 through 473' Processing helix chain 'B' and resid 485 through 493 Processing helix chain 'B' and resid 516 through 526 Processing helix chain 'B' and resid 540 through 553 Processing helix chain 'D' and resid 3 through 18 Processing helix chain 'D' and resid 22 through 31 Processing helix chain 'D' and resid 37 through 50 Processing helix chain 'D' and resid 53 through 66 removed outlier: 3.672A pdb=" N LYS D 58 " --> pdb=" O THR D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 83 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 120 through 134 removed outlier: 4.062A pdb=" N LYS D 134 " --> pdb=" O MET D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 150 removed outlier: 3.623A pdb=" N SER D 149 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N MET D 150 " --> pdb=" O LEU D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 168 removed outlier: 4.261A pdb=" N LYS D 158 " --> pdb=" O ARG D 155 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE D 159 " --> pdb=" O HIS D 156 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TRP D 167 " --> pdb=" O GLU D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 192 removed outlier: 3.568A pdb=" N ALA D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLN D 192 " --> pdb=" O ARG D 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 187 through 192' Processing helix chain 'E' and resid 16 through 24 Processing helix chain 'E' and resid 62 through 70 removed outlier: 4.675A pdb=" N ARG E 66 " --> pdb=" O ASP E 63 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG E 68 " --> pdb=" O ASP E 65 " (cutoff:3.500A) Proline residue: E 69 - end of helix Processing helix chain 'E' and resid 87 through 95 removed outlier: 3.795A pdb=" N ARG E 94 " --> pdb=" O PHE E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 104 Processing helix chain 'E' and resid 123 through 131 Processing helix chain 'E' and resid 139 through 148 Processing helix chain 'E' and resid 165 through 177 Processing helix chain 'H' and resid 62 through 64 No H-bonds generated for 'chain 'H' and resid 62 through 64' Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing sheet with id= A, first strand: chain 'B' and resid 229 through 231 Processing sheet with id= B, 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) Processing sheet with id= C, first strand: chain 'B' and resid 338 through 341 Processing sheet with id= D, first strand: chain 'B' and resid 562 through 567 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) removed outlier: 6.534A pdb=" N LYS B 438 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N LEU B 406 " --> pdb=" O LYS B 438 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N TYR B 440 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLY B 408 " --> pdb=" O TYR B 440 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N TYR B 442 " --> pdb=" O GLY B 408 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 106 through 108 Processing sheet with id= F, first strand: chain 'E' and resid 153 through 156 removed outlier: 3.612A pdb=" N LYS E 153 " --> pdb=" O ILE E 110 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN E 2 " --> pdb=" O PRO E 50 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N GLY E 10 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP E 38 " --> pdb=" O ASP E 57 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'H' and resid 4 through 8 Processing sheet with id= H, first strand: chain 'H' and resid 113 through 115 removed outlier: 4.889A pdb=" N GLY H 50 " --> pdb=" O TRP H 37 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 39 through 41 removed outlier: 3.654A pdb=" N LYS H 45 " --> pdb=" O PHE H 41 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'L' and resid 4 through 6 Processing sheet with id= K, first strand: chain 'L' and resid 10 through 14 removed outlier: 5.756A pdb=" N LYS L 103 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ALA L 13 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N GLU L 105 " --> pdb=" O ALA L 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'L' and resid 84 through 90 removed outlier: 6.132A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LYS L 39 " --> pdb=" O VAL L 44 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N VAL L 44 " --> pdb=" O LYS L 39 " (cutoff:3.500A) 491 hydrogen bonds defined for protein. 1374 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: 3.50 Time building geometry restraints manager: 5.01 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: 122 2.57 - 3.15: 9284 3.15 - 3.74: 18252 3.74 - 4.32: 26032 4.32 - 4.90: 42510 Nonbonded interactions: 96200 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 96195 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: 1.840 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: 7.340 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 32.890 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.000 ------------------------------------------------------------------------------- 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= 0.476 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 : 1.266 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: 1.0838 time to fit residues: 281.7201 Evaluate side-chains 171 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 160 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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: 2.9990 chunk 54 optimal weight: 0.3980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.0980 chunk 52 optimal weight: 0.5980 chunk 101 optimal weight: 0.6980 chunk 39 optimal weight: 0.1980 chunk 61 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 chunk 117 optimal weight: 0.9980 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 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: 0.7552 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10948 Z= 0.219 Angle : 0.647 18.937 14955 Z= 0.291 Chirality : 0.042 0.161 1685 Planarity : 0.004 0.037 1831 Dihedral : 12.148 173.499 1663 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.45 % Allowed : 9.70 % Favored : 86.85 % 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: 1.24 (0.21), residues: 582 sheet: -0.89 (0.32), residues: 229 loop : -0.59 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 380 HIS 0.005 0.001 HIS B 115 PHE 0.025 0.001 PHE B 570 TYR 0.016 0.001 TYR B 201 ARG 0.005 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 198 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 161 time to evaluate : 1.170 Fit side-chains revert: symmetry clash REVERT: B 208 THR cc_start: 0.8318 (p) cc_final: 0.7980 (t) REVERT: B 373 LYS cc_start: 0.7123 (OUTLIER) cc_final: 0.6307 (mptt) REVERT: B 548 LYS cc_start: 0.7954 (mtmm) cc_final: 0.7486 (mmpt) REVERT: D 27 ASP cc_start: 0.7915 (m-30) cc_final: 0.7705 (t0) REVERT: H 49 MET cc_start: 0.8484 (mtp) cc_final: 0.8161 (ttm) REVERT: L 39 LYS cc_start: 0.7829 (mmmt) cc_final: 0.7616 (mptm) outliers start: 37 outliers final: 17 residues processed: 183 average time/residue: 1.1489 time to fit residues: 228.8283 Evaluate side-chains 160 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 142 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 12 ILE 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 414 THR Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 150 THR 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 D residue 205 VAL Chi-restraints excluded: chain E residue 41 SER Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 5 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 97 optimal weight: 0.4980 chunk 79 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 104 optimal weight: 0.0010 chunk 116 optimal weight: 0.0980 chunk 40 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.3786 ------------------------------------------------------------------------------- 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 104 ASN ** D 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 GLN H 44 ASN L 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10948 Z= 0.195 Angle : 0.588 16.403 14955 Z= 0.271 Chirality : 0.041 0.137 1685 Planarity : 0.004 0.035 1831 Dihedral : 11.052 178.099 1651 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.01 % Allowed : 12.78 % Favored : 83.21 % 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: 0.26 (0.23), residues: 1322 helix: 1.25 (0.21), residues: 582 sheet: -0.75 (0.32), residues: 228 loop : -0.54 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 380 HIS 0.006 0.001 HIS B 115 PHE 0.025 0.001 PHE B 570 TYR 0.013 0.001 TYR D 125 ARG 0.006 0.000 ARG E 94 *********************** 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 196 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 153 time to evaluate : 1.178 Fit side-chains revert: symmetry clash REVERT: A 132 THR cc_start: 0.8388 (m) cc_final: 0.8183 (m) REVERT: B 294 LYS cc_start: 0.7206 (ttpp) cc_final: 0.7000 (ttmt) REVERT: B 373 LYS cc_start: 0.7168 (OUTLIER) cc_final: 0.6346 (mptt) REVERT: B 548 LYS cc_start: 0.7968 (mtmm) cc_final: 0.7470 (mmpt) REVERT: C 150 THR cc_start: 0.7864 (OUTLIER) cc_final: 0.7633 (p) REVERT: D 27 ASP cc_start: 0.7925 (m-30) cc_final: 0.7704 (t0) REVERT: D 150 MET cc_start: 0.6213 (OUTLIER) cc_final: 0.5939 (pmm) outliers start: 43 outliers final: 19 residues processed: 182 average time/residue: 1.0707 time to fit residues: 212.4303 Evaluate side-chains 160 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 138 time to evaluate : 1.159 ------------------------------------------------------------------------------- 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 12 ILE Chi-restraints excluded: chain B residue 112 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 B residue 561 VAL Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 150 MET 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 113 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain L residue 5 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 0.5980 chunk 88 optimal weight: 0.1980 chunk 60 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 111 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 ** 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 115 GLN ** D 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2197 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= 0.245 Angle : 0.602 17.310 14955 Z= 0.277 Chirality : 0.041 0.143 1685 Planarity : 0.004 0.040 1831 Dihedral : 10.614 173.655 1648 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.10 % Allowed : 14.09 % Favored : 81.81 % 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: 1.20 (0.21), residues: 580 sheet: -0.66 (0.32), residues: 225 loop : -0.56 (0.27), residues: 517 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 0.029 0.002 PHE B 570 TYR 0.013 0.002 TYR D 125 ARG 0.004 0.001 ARG B 80 *********************** 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 194 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 150 time to evaluate : 1.114 Fit side-chains revert: symmetry clash REVERT: A 132 THR cc_start: 0.8380 (m) cc_final: 0.8162 (m) REVERT: B 373 LYS cc_start: 0.7226 (OUTLIER) cc_final: 0.6407 (mptt) REVERT: B 548 LYS cc_start: 0.7971 (mtmm) cc_final: 0.7469 (mmpt) REVERT: B 568 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7182 (mp0) REVERT: C 150 THR cc_start: 0.7804 (OUTLIER) cc_final: 0.7598 (p) REVERT: D 27 ASP cc_start: 0.7951 (m-30) cc_final: 0.7704 (t0) REVERT: D 150 MET cc_start: 0.6024 (pmm) cc_final: 0.5762 (pmm) REVERT: H 5 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.7263 (mt0) REVERT: H 78 GLN cc_start: 0.8453 (pt0) cc_final: 0.8229 (pt0) outliers start: 44 outliers final: 26 residues processed: 179 average time/residue: 1.0568 time to fit residues: 206.7836 Evaluate side-chains 169 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 139 time to evaluate : 0.963 ------------------------------------------------------------------------------- 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 112 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 360 ASP Chi-restraints excluded: chain B residue 373 LYS Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 414 THR 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 30 SER Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 167 THR 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 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 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: 0.8980 chunk 1 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 0 optimal weight: 1.9990 chunk 63 optimal weight: 0.0040 chunk 111 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 overall best weight: 0.6392 ------------------------------------------------------------------------------- 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 33 GLN ** D 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN ** D 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 ASN L 89 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2384 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= 0.242 Angle : 0.595 17.670 14955 Z= 0.275 Chirality : 0.041 0.144 1685 Planarity : 0.004 0.042 1831 Dihedral : 10.454 167.919 1647 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.01 % Allowed : 14.37 % Favored : 81.62 % 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 (0.22), residues: 1322 helix: 1.17 (0.21), residues: 586 sheet: -0.68 (0.32), residues: 215 loop : -0.66 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 380 HIS 0.007 0.001 HIS B 115 PHE 0.028 0.002 PHE B 570 TYR 0.015 0.001 TYR D 125 ARG 0.005 0.000 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 196 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 153 time to evaluate : 1.217 Fit side-chains revert: symmetry clash REVERT: A 132 THR cc_start: 0.8350 (m) cc_final: 0.8135 (m) REVERT: B 76 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8707 (mp) REVERT: B 321 VAL cc_start: 0.7855 (OUTLIER) cc_final: 0.7625 (m) REVERT: B 373 LYS cc_start: 0.7230 (OUTLIER) cc_final: 0.6428 (mptt) REVERT: B 548 LYS cc_start: 0.7970 (mtmm) cc_final: 0.7454 (mmpt) REVERT: D 27 ASP cc_start: 0.7990 (m-30) cc_final: 0.7695 (t0) REVERT: H 5 GLN cc_start: 0.7633 (OUTLIER) cc_final: 0.7286 (mt0) REVERT: H 78 GLN cc_start: 0.8459 (pt0) cc_final: 0.8242 (pt0) outliers start: 43 outliers final: 25 residues processed: 181 average time/residue: 1.0402 time to fit residues: 205.9916 Evaluate side-chains 173 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 144 time to evaluate : 1.237 ------------------------------------------------------------------------------- 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 76 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 321 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 414 THR Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain D residue 30 SER 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 203 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 167 THR 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 Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 39 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 0.7980 chunk 112 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** D 33 GLN ** D 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN ** D 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 ASN L 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10948 Z= 0.279 Angle : 0.621 18.152 14955 Z= 0.284 Chirality : 0.042 0.156 1685 Planarity : 0.004 0.045 1831 Dihedral : 10.389 162.827 1646 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.92 % Allowed : 15.39 % Favored : 80.69 % 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: 0.07 (0.23), residues: 1322 helix: 1.04 (0.21), residues: 592 sheet: -0.73 (0.32), residues: 222 loop : -0.67 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 380 HIS 0.008 0.002 HIS B 115 PHE 0.031 0.002 PHE B 570 TYR 0.014 0.002 TYR D 81 ARG 0.005 0.001 ARG D 181 *********************** 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 191 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 149 time to evaluate : 1.210 Fit side-chains revert: symmetry clash REVERT: A 132 THR cc_start: 0.8349 (m) cc_final: 0.8136 (m) REVERT: B 203 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7272 (mp0) REVERT: B 294 LYS cc_start: 0.6430 (OUTLIER) cc_final: 0.5593 (mmmt) REVERT: B 373 LYS cc_start: 0.7290 (OUTLIER) cc_final: 0.6475 (mptt) REVERT: B 548 LYS cc_start: 0.7978 (mtmm) cc_final: 0.7452 (mmpt) REVERT: B 568 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.7060 (mp0) REVERT: D 27 ASP cc_start: 0.7992 (m-30) cc_final: 0.7715 (t0) REVERT: H 5 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7287 (mt0) outliers start: 42 outliers final: 27 residues processed: 179 average time/residue: 1.0623 time to fit residues: 207.8206 Evaluate side-chains 176 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 144 time to evaluate : 1.147 ------------------------------------------------------------------------------- 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 112 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 294 LYS 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 414 THR 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 30 SER 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 203 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 3 GLN 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 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: 0.5980 chunk 91 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 69 optimal weight: 0.2980 chunk 124 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 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** ** D 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN L 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2709 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= 0.242 Angle : 0.602 17.889 14955 Z= 0.277 Chirality : 0.041 0.144 1685 Planarity : 0.004 0.044 1831 Dihedral : 10.319 159.043 1646 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.64 % Allowed : 16.04 % 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: 0.09 (0.23), residues: 1322 helix: 1.12 (0.21), residues: 586 sheet: -0.78 (0.32), residues: 228 loop : -0.68 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 36 HIS 0.007 0.001 HIS B 115 PHE 0.028 0.002 PHE B 570 TYR 0.015 0.002 TYR D 81 ARG 0.004 0.000 ARG E 94 *********************** 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 189 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 150 time to evaluate : 1.199 Fit side-chains revert: symmetry clash REVERT: B 203 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7285 (mt-10) REVERT: B 373 LYS cc_start: 0.7317 (OUTLIER) cc_final: 0.6461 (mptt) REVERT: D 27 ASP cc_start: 0.7977 (m-30) cc_final: 0.7703 (t0) REVERT: H 5 GLN cc_start: 0.7644 (OUTLIER) cc_final: 0.7310 (mt0) outliers start: 39 outliers final: 25 residues processed: 177 average time/residue: 1.0599 time to fit residues: 205.4194 Evaluate side-chains 172 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 144 time to evaluate : 1.171 ------------------------------------------------------------------------------- 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 112 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 203 GLU 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 414 THR Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain D residue 30 SER 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 203 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 116 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: 0.9990 chunk 74 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 84 optimal weight: 10.0000 chunk 61 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 97 optimal weight: 0.0040 chunk 113 optimal weight: 0.0270 chunk 119 optimal weight: 1.9990 overall best weight: 0.4250 ------------------------------------------------------------------------------- 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 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 GLN H 16 GLN L 3 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2818 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= 0.202 Angle : 0.592 17.432 14955 Z= 0.272 Chirality : 0.041 0.139 1685 Planarity : 0.004 0.043 1831 Dihedral : 10.201 156.129 1646 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.36 % Allowed : 17.44 % Favored : 79.20 % 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: 0.19 (0.23), residues: 1322 helix: 1.18 (0.21), residues: 588 sheet: -0.61 (0.32), residues: 223 loop : -0.68 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 36 HIS 0.006 0.001 HIS B 115 PHE 0.025 0.001 PHE B 570 TYR 0.015 0.001 TYR D 81 ARG 0.007 0.000 ARG D 188 *********************** 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 180 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 144 time to evaluate : 1.189 Fit side-chains revert: symmetry clash REVERT: B 148 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7715 (tt0) REVERT: B 203 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7623 (mt-10) REVERT: B 373 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.6482 (mptt) REVERT: D 27 ASP cc_start: 0.7949 (m-30) cc_final: 0.7685 (t0) REVERT: D 91 ILE cc_start: 0.7696 (mp) cc_final: 0.7480 (tp) outliers start: 36 outliers final: 23 residues processed: 168 average time/residue: 1.0191 time to fit residues: 187.6358 Evaluate side-chains 166 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 140 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 148 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 203 GLU 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 414 THR Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain D residue 30 SER 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 203 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 5 GLN 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: 2.9990 chunk 119 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 104 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 76 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 HIS 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 ** D 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN L 6 GLN L 89 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 10948 Z= 0.416 Angle : 0.704 19.278 14955 Z= 0.325 Chirality : 0.045 0.163 1685 Planarity : 0.005 0.056 1831 Dihedral : 10.437 155.581 1646 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.82 % Allowed : 16.98 % Favored : 79.20 % 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: -0.14 (0.22), residues: 1322 helix: 0.82 (0.21), residues: 594 sheet: -0.75 (0.32), residues: 226 loop : -0.75 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 36 HIS 0.009 0.002 HIS B 115 PHE 0.038 0.002 PHE B 570 TYR 0.015 0.002 TYR B 401 ARG 0.006 0.001 ARG D 188 *********************** 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 185 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 144 time to evaluate : 1.330 Fit side-chains revert: symmetry clash REVERT: B 148 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7739 (tt0) REVERT: B 203 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7548 (mt-10) REVERT: B 373 LYS cc_start: 0.7427 (OUTLIER) cc_final: 0.6545 (mptt) REVERT: D 27 ASP cc_start: 0.8038 (m-30) cc_final: 0.7736 (t0) REVERT: E 171 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7482 (mp0) outliers start: 41 outliers final: 27 residues processed: 173 average time/residue: 1.0203 time to fit residues: 192.7879 Evaluate side-chains 169 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 138 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 148 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 203 GLU 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 414 THR 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 30 SER Chi-restraints excluded: chain D residue 67 ASP 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 203 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 171 GLU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain L residue 39 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 85 optimal weight: 10.0000 chunk 128 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 79 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 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 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 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN L 3 GLN L 6 GLN L 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10948 Z= 0.275 Angle : 0.649 18.993 14955 Z= 0.298 Chirality : 0.042 0.148 1685 Planarity : 0.004 0.048 1831 Dihedral : 10.373 153.947 1646 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.71 % Allowed : 18.75 % Favored : 78.54 % 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: -0.10 (0.22), residues: 1322 helix: 0.93 (0.21), residues: 585 sheet: -0.78 (0.32), residues: 225 loop : -0.78 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 36 HIS 0.007 0.002 HIS D 69 PHE 0.031 0.002 PHE B 570 TYR 0.014 0.002 TYR D 81 ARG 0.006 0.001 ARG D 188 ********************** 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 168 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 139 time to evaluate : 1.218 Fit side-chains revert: symmetry clash REVERT: B 148 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7733 (tt0) REVERT: B 203 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7480 (mt-10) REVERT: B 373 LYS cc_start: 0.7500 (OUTLIER) cc_final: 0.6649 (mptt) REVERT: D 27 ASP cc_start: 0.7941 (m-30) cc_final: 0.7694 (t0) REVERT: D 184 ARG cc_start: 0.8478 (mmm-85) cc_final: 0.8054 (mpt90) REVERT: E 171 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7456 (mp0) outliers start: 29 outliers final: 22 residues processed: 158 average time/residue: 1.0881 time to fit residues: 188.9527 Evaluate side-chains 162 residues out of total 1150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 136 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 148 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 203 GLU 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 414 THR Chi-restraints excluded: chain D residue 30 SER 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 203 THR Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 167 THR 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 5 GLN Chi-restraints excluded: chain L residue 39 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 0.0670 chunk 94 optimal weight: 0.0870 chunk 15 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 105 optimal weight: 0.0770 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.3254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 HIS ** 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 ** D 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN L 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.135648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.110844 restraints weight = 15484.117| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.82 r_work: 0.3403 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3048 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= 0.187 Angle : 0.591 17.601 14955 Z= 0.276 Chirality : 0.041 0.136 1685 Planarity : 0.004 0.045 1831 Dihedral : 10.155 151.585 1646 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.24 % Allowed : 19.50 % Favored : 78.26 % 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: 0.12 (0.23), residues: 1322 helix: 1.10 (0.21), residues: 588 sheet: -0.67 (0.32), residues: 223 loop : -0.68 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 36 HIS 0.006 0.001 HIS B 338 PHE 0.023 0.001 PHE B 570 TYR 0.015 0.001 TYR D 81 ARG 0.008 0.000 ARG D 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4243.65 seconds wall clock time: 75 minutes 42.07 seconds (4542.07 seconds total)