Starting phenix.real_space_refine on Sun Aug 4 09:14:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kei_37159/08_2024/8kei_37159.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kei_37159/08_2024/8kei_37159.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kei_37159/08_2024/8kei_37159.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kei_37159/08_2024/8kei_37159.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kei_37159/08_2024/8kei_37159.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kei_37159/08_2024/8kei_37159.cif" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.048 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: 6 Type Number sf(0) Gaussians Fe 2 7.16 5 P 2 5.49 5 S 49 5.16 5 C 6606 2.51 5 N 1689 2.21 5 O 1861 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 5": "OE1" <-> "OE2" Residue "A PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 540": "OE1" <-> "OE2" Residue "D GLU 114": "OE1" <-> "OE2" Residue "D GLU 151": "OE1" <-> "OE2" Residue "E GLU 127": "OE1" <-> "OE2" Residue "E GLU 169": "OE1" <-> "OE2" 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: 10209 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1035 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain: "B" Number of atoms: 4318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4318 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 22, 'TRANS': 511} Chain breaks: 2 Chain: "C" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1648 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "D" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1304 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain: "E" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1652 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 10, 'TRANS': 206} 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: "G" 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: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-2': 1, 'POV:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 148 Unusual residues: {'HEM': 2, 'LBN': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.80, per 1000 atoms: 0.76 Number of scatterers: 10209 At special positions: 0 Unit cell: (73.1, 102.85, 204, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 2 26.01 S 49 16.00 P 2 15.00 O 1861 8.00 N 1689 7.00 C 6606 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 244 " - pdb=" SG CYS B 257 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 36 " - pdb=" SG CYS C 51 " distance=2.01 Simple disulfide: pdb=" SG CYS C 149 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.04 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 198 " distance=2.03 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 G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " NAG-ASN " NAG B 603 " - " ASN B 132 " " NAG F 1 " - " ASN B 240 " " NAG G 1 " - " ASN B 149 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.83 Conformation dependent library (CDL) restraints added in 1.9 seconds 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2352 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 18 sheets defined 34.4% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 36 through 53 removed outlier: 3.687A pdb=" N GLU A 53 " --> pdb=" O VAL A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 78 removed outlier: 3.533A pdb=" N THR A 74 " --> pdb=" O GLN A 70 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N VAL A 76 " --> pdb=" O TYR A 72 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A 78 " --> pdb=" O THR A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 98 removed outlier: 3.537A pdb=" N SER A 98 " --> pdb=" O HIS A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 103 removed outlier: 4.144A pdb=" N PHE A 103 " --> pdb=" O PRO A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 128 removed outlier: 4.065A pdb=" N ALA A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY A 128 " --> pdb=" O ALA A 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 35 Processing helix chain 'B' and resid 36 through 39 removed outlier: 3.543A pdb=" N PHE B 39 " --> pdb=" O PRO B 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 36 through 39' Processing helix chain 'B' and resid 40 through 47 Processing helix chain 'B' and resid 48 through 81 removed outlier: 3.691A pdb=" N LEU B 52 " --> pdb=" O SER B 48 " (cutoff:3.500A) Proline residue: B 56 - end of helix removed outlier: 3.707A pdb=" N PHE B 62 " --> pdb=" O ALA B 58 " (cutoff:3.500A) Proline residue: B 70 - end of helix Processing helix chain 'B' and resid 96 through 131 removed outlier: 3.667A pdb=" N GLU B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TRP B 125 " --> pdb=" O PHE B 121 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG B 130 " --> pdb=" O CYS B 126 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL B 131 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 143 Processing helix chain 'B' and resid 164 through 173 Processing helix chain 'B' and resid 176 through 193 Processing helix chain 'B' and resid 207 through 210 Processing helix chain 'B' and resid 211 through 223 removed outlier: 3.672A pdb=" N GLY B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 240 removed outlier: 3.830A pdb=" N ALA B 237 " --> pdb=" O ALA B 233 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL B 238 " --> pdb=" O GLU B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 251 removed outlier: 4.113A pdb=" N TRP B 251 " --> pdb=" O ILE B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 291 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 413 through 430 removed outlier: 3.755A pdb=" N ALA B 417 " --> pdb=" O VAL B 413 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER B 418 " --> pdb=" O THR B 414 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE B 419 " --> pdb=" O PRO B 415 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TRP B 424 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N TYR B 425 " --> pdb=" O LYS B 421 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS B 426 " --> pdb=" O SER B 422 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR B 427 " --> pdb=" O VAL B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 463 removed outlier: 3.729A pdb=" N ALA B 455 " --> pdb=" O PHE B 451 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU B 457 " --> pdb=" O TRP B 453 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN B 459 " --> pdb=" O ALA B 455 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER B 463 " --> pdb=" O GLN B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 469 removed outlier: 3.567A pdb=" N ARG B 468 " --> pdb=" O MET B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 525 removed outlier: 3.668A pdb=" N THR B 522 " --> pdb=" O ASN B 518 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE B 523 " --> pdb=" O GLU B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 554 removed outlier: 3.927A pdb=" N SER B 547 " --> pdb=" O ALA B 543 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N GLN B 549 " --> pdb=" O THR B 545 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER B 550 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE B 551 " --> pdb=" O SER B 547 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER B 552 " --> pdb=" O LYS B 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 66 removed outlier: 3.695A pdb=" N LYS C 66 " --> pdb=" O ARG C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 200 removed outlier: 3.526A pdb=" N GLY C 199 " --> pdb=" O SER C 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 40 removed outlier: 3.566A pdb=" N TRP D 24 " --> pdb=" O GLY D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 62 removed outlier: 3.895A pdb=" N PHE D 50 " --> pdb=" O GLY D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 91 Processing helix chain 'D' and resid 92 through 94 No H-bonds generated for 'chain 'D' and resid 92 through 94' Processing helix chain 'D' and resid 146 through 162 Processing helix chain 'E' and resid 125 through 131 Processing helix chain 'E' and resid 186 through 191 removed outlier: 4.679A pdb=" N GLU E 191 " --> pdb=" O LYS E 187 " (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 296 through 301 removed outlier: 5.731A pdb=" N ILE B 297 " --> pdb=" O LYS B 313 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LYS B 313 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU B 310 " --> pdb=" O ILE B 353 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 386 through 387 removed outlier: 5.984A pdb=" N TRP B 337 " --> pdb=" O VAL D 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 404 through 407 removed outlier: 3.910A pdb=" N VAL B 407 " --> pdb=" O PHE B 535 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE B 532 " --> pdb=" O ILE B 564 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 443 through 445 removed outlier: 6.123A pdb=" N TRP B 443 " --> pdb=" O TYR B 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain 'C' and resid 46 through 53 removed outlier: 7.359A pdb=" N TRP C 37 " --> pdb=" O ILE C 49 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N CYS C 51 " --> pdb=" O MET C 35 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N MET C 35 " --> pdb=" O CYS C 51 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG C 98 " --> pdb=" O ASP C 110 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 144 through 151 Processing sheet with id=AA9, first strand: chain 'C' and resid 144 through 151 Processing sheet with id=AB1, first strand: chain 'C' and resid 160 through 163 removed outlier: 3.787A pdb=" N THR C 160 " --> pdb=" O ASN C 208 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN C 206 " --> pdb=" O SER C 162 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 4 through 5 Processing sheet with id=AB3, first strand: chain 'D' and resid 107 through 116 removed outlier: 3.829A pdb=" N ASP D 109 " --> pdb=" O ARG D 129 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET D 125 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 107 through 116 removed outlier: 3.829A pdb=" N ASP D 109 " --> pdb=" O ARG D 129 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET D 125 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 5 through 7 removed outlier: 3.638A pdb=" N VAL E 20 " --> pdb=" O ILE E 76 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 13 through 15 removed outlier: 6.690A pdb=" N ALA E 14 " --> pdb=" O LYS E 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'E' and resid 46 through 50 removed outlier: 6.679A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N TYR E 50 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 118 through 122 removed outlier: 6.181A pdb=" N TYR E 177 " --> pdb=" O ASN E 142 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 157 through 158 removed outlier: 3.663A pdb=" N PHE E 213 " --> pdb=" O TYR E 196 " (cutoff:3.500A) 409 hydrogen bonds defined for protein. 1134 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: 3.87 Time building geometry restraints manager: 6.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.37: 3238 1.37 - 1.54: 6988 1.54 - 1.71: 171 1.71 - 1.88: 67 1.88 - 2.05: 8 Bond restraints: 10472 Sorted by residual: bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.623 -0.104 2.00e-02 2.50e+03 2.68e+01 bond pdb=" CA VAL B 413 " pdb=" C VAL B 413 " ideal model delta sigma weight residual 1.523 1.461 0.061 1.31e-02 5.83e+03 2.19e+01 bond pdb=" CA THR B 414 " pdb=" C THR B 414 " ideal model delta sigma weight residual 1.524 1.472 0.052 1.26e-02 6.30e+03 1.72e+01 bond pdb=" CA ILE B 411 " pdb=" C ILE B 411 " ideal model delta sigma weight residual 1.520 1.471 0.049 1.26e-02 6.30e+03 1.48e+01 bond pdb=" CA ARG B 287 " pdb=" C ARG B 287 " ideal model delta sigma weight residual 1.523 1.470 0.053 1.37e-02 5.33e+03 1.48e+01 ... (remaining 10467 not shown) Histogram of bond angle deviations from ideal: 89.49 - 106.95: 304 106.95 - 124.40: 13594 124.40 - 141.86: 332 141.86 - 159.31: 0 159.31 - 176.77: 4 Bond angle restraints: 14234 Sorted by residual: angle pdb=" N VAL B 413 " pdb=" CA VAL B 413 " pdb=" C VAL B 413 " ideal model delta sigma weight residual 112.17 105.08 7.09 9.50e-01 1.11e+00 5.57e+01 angle pdb=" C THR B 414 " pdb=" N PRO B 415 " pdb=" CA PRO B 415 " ideal model delta sigma weight residual 119.56 113.36 6.20 1.01e+00 9.80e-01 3.76e+01 angle pdb=" C GLY B 275 " pdb=" N PRO B 276 " pdb=" CA PRO B 276 " ideal model delta sigma weight residual 119.05 112.50 6.55 1.11e+00 8.12e-01 3.48e+01 angle pdb=" N SER B 291 " pdb=" CA SER B 291 " pdb=" C SER B 291 " ideal model delta sigma weight residual 112.59 119.49 -6.90 1.22e+00 6.72e-01 3.20e+01 angle pdb=" C VAL B 286 " pdb=" CA VAL B 286 " pdb=" CB VAL B 286 " ideal model delta sigma weight residual 112.16 104.02 8.14 1.55e+00 4.16e-01 2.76e+01 ... (remaining 14229 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.23: 5879 32.23 - 64.46: 285 64.46 - 96.69: 32 96.69 - 128.92: 7 128.92 - 161.15: 1 Dihedral angle restraints: 6204 sinusoidal: 2533 harmonic: 3671 Sorted by residual: dihedral pdb=" CA MET C 35 " pdb=" C MET C 35 " pdb=" N CYS C 36 " pdb=" CA CYS C 36 " ideal model delta harmonic sigma weight residual -180.00 -155.77 -24.23 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" O5 LBN B 604 " pdb=" C2 LBN B 604 " pdb=" C3 LBN B 604 " pdb=" O7 LBN B 604 " ideal model delta sinusoidal sigma weight residual 62.67 -98.48 161.15 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" CA ASP B 95 " pdb=" C ASP B 95 " pdb=" N ARG B 96 " pdb=" CA ARG B 96 " ideal model delta harmonic sigma weight residual 180.00 158.38 21.62 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 6201 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1512 0.090 - 0.180: 80 0.180 - 0.270: 3 0.270 - 0.361: 2 0.361 - 0.451: 1 Chirality restraints: 1598 Sorted by residual: chirality pdb=" C1 NAG B 603 " pdb=" ND2 ASN B 132 " pdb=" C2 NAG B 603 " pdb=" O5 NAG B 603 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.08e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN B 240 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN B 149 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 1595 not shown) Planarity restraints: 1749 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 527 " -0.069 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO B 528 " 0.176 5.00e-02 4.00e+02 pdb=" CA PRO B 528 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 528 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 272 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.67e+00 pdb=" C TRP B 272 " -0.028 2.00e-02 2.50e+03 pdb=" O TRP B 272 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE B 273 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 96 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.67e+00 pdb=" C ARG B 96 " 0.028 2.00e-02 2.50e+03 pdb=" O ARG B 96 " -0.010 2.00e-02 2.50e+03 pdb=" N ASN B 97 " -0.010 2.00e-02 2.50e+03 ... (remaining 1746 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 328 2.70 - 3.25: 9871 3.25 - 3.80: 15524 3.80 - 4.35: 18558 4.35 - 4.90: 32103 Nonbonded interactions: 76384 Sorted by model distance: nonbonded pdb=" O ARG B 559 " pdb=" NH1 ARG B 559 " model vdw 2.150 3.120 nonbonded pdb=" O3 NAG G 2 " pdb=" O2 BMA G 3 " model vdw 2.196 3.040 nonbonded pdb=" OE1 GLU A 53 " pdb=" OH TYR A 121 " model vdw 2.201 3.040 nonbonded pdb=" OH TYR D 2 " pdb=" OG1 THR D 139 " model vdw 2.205 3.040 nonbonded pdb=" OE2 GLU C 6 " pdb=" OG1 THR C 116 " model vdw 2.224 3.040 ... (remaining 76379 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 Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'G' } 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 group one per residue 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: 4.940 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: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 36.750 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.120 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:3.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 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 : 0.004 0.104 10472 Z= 0.279 Angle : 0.727 10.455 14234 Z= 0.380 Chirality : 0.045 0.451 1598 Planarity : 0.004 0.102 1746 Dihedral : 18.448 161.154 3834 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.46 % Allowed : 32.96 % Favored : 66.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.29 (0.25), residues: 1258 helix: 1.41 (0.28), residues: 386 sheet: 0.19 (0.35), residues: 265 loop : -1.48 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 37 HIS 0.009 0.001 HIS B 119 PHE 0.019 0.001 PHE B 520 TYR 0.012 0.001 TYR A 121 ARG 0.019 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 136 time to evaluate : 1.633 Fit side-chains revert: symmetry clash REVERT: B 465 MET cc_start: 0.7743 (ptm) cc_final: 0.7513 (ttp) outliers start: 5 outliers final: 4 residues processed: 140 average time/residue: 0.2170 time to fit residues: 44.6984 Evaluate side-chains 131 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 127 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain C residue 56 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 113 optimal weight: 0.0270 overall best weight: 1.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 HIS B 338 HIS B 477 ASN B 518 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 10472 Z= 0.294 Angle : 0.654 8.335 14234 Z= 0.323 Chirality : 0.043 0.374 1598 Planarity : 0.004 0.067 1746 Dihedral : 10.405 150.149 1599 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 4.63 % Allowed : 30.28 % Favored : 65.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.29 (0.25), residues: 1258 helix: 1.32 (0.28), residues: 389 sheet: -0.01 (0.34), residues: 277 loop : -1.33 (0.27), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 37 HIS 0.008 0.001 HIS B 119 PHE 0.018 0.001 PHE B 62 TYR 0.012 0.001 TYR E 144 ARG 0.004 0.000 ARG B 559 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 142 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 122 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8149 (ttpp) REVERT: E 102 PHE cc_start: 0.9065 (OUTLIER) cc_final: 0.7421 (t80) REVERT: E 199 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7479 (mm-30) outliers start: 50 outliers final: 32 residues processed: 186 average time/residue: 0.2075 time to fit residues: 55.8956 Evaluate side-chains 166 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 132 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain C residue 2 GLN Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 36 CYS Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 102 PHE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 180 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 101 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 GLN C 201 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10472 Z= 0.253 Angle : 0.623 10.057 14234 Z= 0.305 Chirality : 0.042 0.332 1598 Planarity : 0.004 0.066 1746 Dihedral : 9.124 143.847 1597 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 6.30 % Allowed : 28.98 % Favored : 64.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.25), residues: 1258 helix: 1.39 (0.28), residues: 389 sheet: 0.00 (0.34), residues: 279 loop : -1.37 (0.27), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 163 HIS 0.008 0.001 HIS B 119 PHE 0.015 0.001 PHE B 62 TYR 0.014 0.001 TYR D 86 ARG 0.004 0.000 ARG D 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 134 time to evaluate : 1.183 Fit side-chains revert: symmetry clash REVERT: B 60 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8174 (tt) REVERT: D 122 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8134 (ttpp) REVERT: E 102 PHE cc_start: 0.9064 (OUTLIER) cc_final: 0.7464 (t80) outliers start: 68 outliers final: 42 residues processed: 190 average time/residue: 0.1989 time to fit residues: 54.9021 Evaluate side-chains 173 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 128 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 94 HIS Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 428 CYS Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain C residue 2 GLN Chi-restraints excluded: chain C residue 36 CYS Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain E residue 102 PHE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 196 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 10472 Z= 0.348 Angle : 0.674 11.218 14234 Z= 0.332 Chirality : 0.043 0.323 1598 Planarity : 0.004 0.066 1746 Dihedral : 8.733 138.141 1596 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 7.04 % Allowed : 28.61 % Favored : 64.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.41 (0.25), residues: 1258 helix: 1.28 (0.27), residues: 388 sheet: -0.15 (0.34), residues: 282 loop : -1.41 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 163 HIS 0.012 0.002 HIS B 222 PHE 0.021 0.002 PHE B 62 TYR 0.014 0.001 TYR E 144 ARG 0.002 0.000 ARG D 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 133 time to evaluate : 1.272 Fit side-chains revert: symmetry clash REVERT: B 60 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8167 (tt) REVERT: D 122 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8159 (ttpp) outliers start: 76 outliers final: 53 residues processed: 195 average time/residue: 0.2011 time to fit residues: 57.1729 Evaluate side-chains 182 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 127 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 384 LYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 428 CYS Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain C residue 2 GLN Chi-restraints excluded: chain C residue 36 CYS Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 218 LYS Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 102 PHE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 196 TYR Chi-restraints excluded: chain E residue 210 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10472 Z= 0.251 Angle : 0.638 9.704 14234 Z= 0.312 Chirality : 0.042 0.304 1598 Planarity : 0.004 0.073 1746 Dihedral : 8.512 134.358 1596 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 6.11 % Allowed : 29.54 % Favored : 64.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.25), residues: 1258 helix: 1.50 (0.28), residues: 382 sheet: -0.19 (0.33), residues: 287 loop : -1.30 (0.27), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 163 HIS 0.007 0.001 HIS B 119 PHE 0.017 0.001 PHE B 520 TYR 0.013 0.001 TYR B 427 ARG 0.007 0.000 ARG D 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 132 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8485 (mt0) REVERT: B 60 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8146 (tt) REVERT: B 268 MET cc_start: 0.8794 (ppp) cc_final: 0.8584 (ppp) REVERT: D 114 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7913 (mm-30) REVERT: D 122 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8201 (ttpp) REVERT: E 102 PHE cc_start: 0.9073 (OUTLIER) cc_final: 0.7459 (t80) outliers start: 66 outliers final: 52 residues processed: 188 average time/residue: 0.1995 time to fit residues: 54.4351 Evaluate side-chains 185 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 129 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 428 CYS Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain C residue 2 GLN Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 36 CYS Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 218 LYS Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 102 PHE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 196 TYR Chi-restraints excluded: chain E residue 210 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 116 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10472 Z= 0.246 Angle : 0.638 10.188 14234 Z= 0.310 Chirality : 0.042 0.295 1598 Planarity : 0.004 0.067 1746 Dihedral : 8.363 130.679 1596 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 6.94 % Allowed : 29.81 % Favored : 63.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.25 (0.25), residues: 1258 helix: 1.52 (0.28), residues: 383 sheet: -0.18 (0.33), residues: 285 loop : -1.31 (0.27), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 163 HIS 0.010 0.001 HIS B 119 PHE 0.025 0.001 PHE C 131 TYR 0.016 0.001 TYR D 86 ARG 0.005 0.000 ARG D 118 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 132 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8492 (mt0) REVERT: B 60 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8153 (tt) REVERT: B 161 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7077 (ttpp) REVERT: D 114 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7951 (mm-30) REVERT: D 122 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8217 (ttpp) REVERT: E 102 PHE cc_start: 0.9055 (OUTLIER) cc_final: 0.7451 (t80) outliers start: 75 outliers final: 58 residues processed: 195 average time/residue: 0.1977 time to fit residues: 56.0545 Evaluate side-chains 195 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 132 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 532 ILE Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain C residue 2 GLN Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 36 CYS Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 218 LYS Chi-restraints excluded: chain D residue 39 TYR Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 102 PHE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 196 TYR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 210 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 120 optimal weight: 5.9990 chunk 75 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 48 optimal weight: 0.0020 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10472 Z= 0.198 Angle : 0.619 9.010 14234 Z= 0.299 Chirality : 0.041 0.279 1598 Planarity : 0.004 0.071 1746 Dihedral : 8.119 125.708 1596 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 5.65 % Allowed : 31.48 % Favored : 62.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.25), residues: 1258 helix: 1.52 (0.28), residues: 394 sheet: -0.20 (0.33), residues: 287 loop : -1.27 (0.28), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 337 HIS 0.008 0.001 HIS B 119 PHE 0.017 0.001 PHE B 520 TYR 0.014 0.001 TYR B 427 ARG 0.007 0.000 ARG D 118 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 137 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.8482 (mt0) REVERT: B 60 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8053 (tt) REVERT: B 161 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7068 (ttpp) REVERT: D 114 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7946 (mm-30) REVERT: D 122 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8218 (ttpp) REVERT: E 102 PHE cc_start: 0.9032 (OUTLIER) cc_final: 0.7486 (t80) outliers start: 61 outliers final: 49 residues processed: 185 average time/residue: 0.2030 time to fit residues: 54.7963 Evaluate side-chains 186 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 132 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 465 MET Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain C residue 2 GLN Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 36 CYS Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 218 LYS Chi-restraints excluded: chain D residue 39 TYR Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 102 PHE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 196 TYR Chi-restraints excluded: chain E residue 210 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 0.6980 chunk 36 optimal weight: 6.9990 chunk 23 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 109 optimal weight: 0.0670 chunk 115 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10472 Z= 0.220 Angle : 0.625 9.571 14234 Z= 0.302 Chirality : 0.041 0.273 1598 Planarity : 0.004 0.070 1746 Dihedral : 7.994 121.027 1596 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 6.30 % Allowed : 31.20 % Favored : 62.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.25), residues: 1258 helix: 1.54 (0.28), residues: 393 sheet: -0.12 (0.33), residues: 278 loop : -1.34 (0.27), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 163 HIS 0.008 0.001 HIS B 119 PHE 0.019 0.001 PHE B 520 TYR 0.017 0.001 TYR D 86 ARG 0.007 0.000 ARG D 118 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 141 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8481 (mt0) REVERT: B 60 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8094 (tt) REVERT: B 161 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7127 (ttpp) REVERT: D 114 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7975 (mm-30) REVERT: D 122 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8227 (ttpp) REVERT: E 102 PHE cc_start: 0.9064 (OUTLIER) cc_final: 0.7450 (t80) outliers start: 68 outliers final: 58 residues processed: 197 average time/residue: 0.1974 time to fit residues: 56.8547 Evaluate side-chains 202 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 139 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 384 LYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain C residue 2 GLN Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 36 CYS Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 218 LYS Chi-restraints excluded: chain D residue 39 TYR Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 102 PHE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 196 TYR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 210 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 101 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 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 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10472 Z= 0.216 Angle : 0.636 11.127 14234 Z= 0.306 Chirality : 0.041 0.268 1598 Planarity : 0.004 0.074 1746 Dihedral : 7.899 117.020 1596 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 6.20 % Allowed : 31.39 % Favored : 62.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.25), residues: 1258 helix: 1.57 (0.28), residues: 392 sheet: -0.15 (0.33), residues: 280 loop : -1.33 (0.27), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 163 HIS 0.008 0.001 HIS B 119 PHE 0.019 0.001 PHE B 520 TYR 0.015 0.001 TYR B 427 ARG 0.006 0.000 ARG D 118 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 138 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8491 (mt0) REVERT: B 60 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8089 (tt) REVERT: B 161 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7128 (ttpp) REVERT: D 114 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7993 (mm-30) REVERT: D 122 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8267 (ttpp) REVERT: E 3 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7677 (tt) REVERT: E 102 PHE cc_start: 0.9045 (OUTLIER) cc_final: 0.7498 (t80) outliers start: 67 outliers final: 57 residues processed: 194 average time/residue: 0.2048 time to fit residues: 57.4934 Evaluate side-chains 197 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 134 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain C residue 2 GLN Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 36 CYS Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 218 LYS Chi-restraints excluded: chain D residue 39 TYR Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 102 PHE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 196 TYR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 210 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 0.9980 chunk 56 optimal weight: 0.0570 chunk 82 optimal weight: 0.2980 chunk 124 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10472 Z= 0.201 Angle : 0.639 11.277 14234 Z= 0.308 Chirality : 0.041 0.262 1598 Planarity : 0.004 0.073 1746 Dihedral : 7.790 112.136 1596 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 5.74 % Allowed : 31.94 % Favored : 62.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.22 (0.25), residues: 1258 helix: 1.51 (0.28), residues: 398 sheet: -0.13 (0.33), residues: 283 loop : -1.35 (0.27), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 163 HIS 0.008 0.001 HIS B 119 PHE 0.020 0.001 PHE B 520 TYR 0.012 0.001 TYR A 121 ARG 0.007 0.000 ARG B 559 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 140 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 TYR cc_start: 0.8348 (m-80) cc_final: 0.7808 (m-80) REVERT: A 130 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8486 (mt0) REVERT: B 60 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8072 (tt) REVERT: B 161 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7130 (ttpp) REVERT: D 114 GLU cc_start: 0.8236 (mm-30) cc_final: 0.8015 (mm-30) REVERT: D 122 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8264 (ttpp) REVERT: E 3 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7676 (tt) REVERT: E 102 PHE cc_start: 0.9026 (OUTLIER) cc_final: 0.7475 (t80) outliers start: 62 outliers final: 55 residues processed: 191 average time/residue: 0.1949 time to fit residues: 54.2607 Evaluate side-chains 195 residues out of total 1080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 134 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 119 HIS Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 210 HIS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 384 LYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain C residue 2 GLN Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 36 CYS Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 218 LYS Chi-restraints excluded: chain D residue 39 TYR Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 102 PHE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 128 GLN Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 196 TYR Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 210 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 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 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.145032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.117910 restraints weight = 16980.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.117965 restraints weight = 13614.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.119171 restraints weight = 13961.575| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10472 Z= 0.222 Angle : 0.651 11.810 14234 Z= 0.312 Chirality : 0.041 0.259 1598 Planarity : 0.004 0.073 1746 Dihedral : 7.740 108.174 1596 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 5.83 % Allowed : 31.76 % Favored : 62.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.25), residues: 1258 helix: 1.59 (0.28), residues: 393 sheet: -0.16 (0.33), residues: 284 loop : -1.34 (0.27), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 163 HIS 0.008 0.001 HIS B 119 PHE 0.020 0.001 PHE B 520 TYR 0.016 0.001 TYR B 427 ARG 0.008 0.000 ARG B 559 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2264.50 seconds wall clock time: 41 minutes 13.94 seconds (2473.94 seconds total)