Starting phenix.real_space_refine on Tue Sep 24 23:53:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxd_24729/09_2024/7rxd_24729.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxd_24729/09_2024/7rxd_24729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxd_24729/09_2024/7rxd_24729.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxd_24729/09_2024/7rxd_24729.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxd_24729/09_2024/7rxd_24729.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxd_24729/09_2024/7rxd_24729.cif" } resolution = 3.6 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= 0.000 sd= 0.004 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: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 5749 2.51 5 N 1490 2.21 5 O 1737 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9007 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 3433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3433 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 24, 'TRANS': 414} Chain breaks: 4 Chain: "H" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1582 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 192} Chain breaks: 2 Chain: "L" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1588 Classifications: {'peptide': 204} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 194} Chain breaks: 2 Chain: "N" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 990 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 121} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1391 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 9, 'TRANS': 163} Chain breaks: 2 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.60, per 1000 atoms: 0.62 Number of scatterers: 9007 At special positions: 0 Unit cell: (118.72, 133.56, 111.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 1737 8.00 N 1490 7.00 C 5749 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.04 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.05 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " GLC A 1 " - " GLC A 2 " Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 1.1 seconds 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 22 sheets defined 27.9% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'B' and resid 17 through 28 Processing helix chain 'B' and resid 43 through 52 Proline residue: B 49 - end of helix Processing helix chain 'B' and resid 64 through 74 removed outlier: 4.055A pdb=" N PHE B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY B 69 " --> pdb=" O HIS B 65 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY B 70 " --> pdb=" O ASP B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 89 Processing helix chain 'B' and resid 91 through 98 removed outlier: 3.553A pdb=" N TRP B 95 " --> pdb=" O TYR B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 141 removed outlier: 4.490A pdb=" N ALA B 135 " --> pdb=" O GLU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 164 removed outlier: 3.923A pdb=" N THR B 158 " --> pdb=" O GLU B 154 " (cutoff:3.500A) Proline residue: B 160 - end of helix Processing helix chain 'B' and resid 182 through 185 removed outlier: 4.399A pdb=" N ASP B 185 " --> pdb=" O VAL B 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 182 through 185' Processing helix chain 'B' and resid 186 through 202 Processing helix chain 'B' and resid 210 through 220 Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'B' and resid 232 through 240 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 287 through 298 removed outlier: 3.640A pdb=" N ASP B 297 " --> pdb=" O ALA B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 313 Processing helix chain 'B' and resid 315 through 328 Processing helix chain 'B' and resid 336 through 353 removed outlier: 3.913A pdb=" N PHE B 340 " --> pdb=" O GLN B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 370 removed outlier: 3.610A pdb=" N MET B 370 " --> pdb=" O GLN B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 388 Processing helix chain 'B' and resid 391 through 406 Processing helix chain 'B' and resid 502 through 517 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.568A pdb=" N PHE H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.798A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 85 through 89 Processing helix chain 'L' and resid 126 through 133 Processing helix chain 'L' and resid 188 through 194 removed outlier: 3.722A pdb=" N HIS L 194 " --> pdb=" O ASP L 190 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.531A pdb=" N LYS N 65 " --> pdb=" O ASP N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 337 through 343 removed outlier: 3.748A pdb=" N VAL R 341 " --> pdb=" O PRO R 337 " (cutoff:3.500A) Processing helix chain 'R' and resid 365 through 370 Processing helix chain 'R' and resid 383 through 387 removed outlier: 3.798A pdb=" N LEU R 387 " --> pdb=" O PRO R 384 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 410 removed outlier: 4.935A pdb=" N ARG R 408 " --> pdb=" O ASP R 405 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 422 Processing helix chain 'R' and resid 438 through 443 Processing helix chain 'R' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'B' and resid 37 through 39 removed outlier: 5.958A pdb=" N ILE B 10 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL B 9 " --> pdb=" O ILE B 60 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N PHE B 62 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N TRP B 11 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ALA B 265 " --> pdb=" O PRO B 108 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 37 through 39 removed outlier: 5.958A pdb=" N ILE B 10 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL B 9 " --> pdb=" O ILE B 60 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N PHE B 62 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N TRP B 11 " --> pdb=" O PHE B 62 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 99 through 100 Processing sheet with id=AA4, first strand: chain 'B' and resid 225 through 228 Processing sheet with id=AA5, first strand: chain 'B' and resid 171 through 173 removed outlier: 4.055A pdb=" N LYS B 171 " --> pdb=" O ASP B 178 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 250 through 251 Processing sheet with id=AA7, first strand: chain 'B' and resid 522 through 526 Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.770A pdb=" N GLY H 33 " --> pdb=" O ARG H 99 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 130 through 134 removed outlier: 4.043A pdb=" N GLY H 149 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 130 through 134 removed outlier: 4.043A pdb=" N GLY H 149 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.835A pdb=" N LEU L 11 " --> pdb=" O GLU L 110 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N LYS L 112 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL L 13 " --> pdb=" O LYS L 112 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU L 39 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N TYR L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.835A pdb=" N LEU L 11 " --> pdb=" O GLU L 110 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N LYS L 112 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL L 13 " --> pdb=" O LYS L 112 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 119 through 123 removed outlier: 5.682A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 150 through 154 Processing sheet with id=AB8, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB9, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.299A pdb=" N GLY N 10 " --> pdb=" O THR N 118 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N SER N 120 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL N 12 " --> pdb=" O SER N 120 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N LYS N 99 " --> pdb=" O ARG N 33 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ARG N 33 " --> pdb=" O LYS N 99 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N MET N 34 " --> pdb=" O ALA N 50 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.299A pdb=" N GLY N 10 " --> pdb=" O THR N 118 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N SER N 120 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL N 12 " --> pdb=" O SER N 120 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'R' and resid 354 through 358 removed outlier: 3.921A pdb=" N VAL R 395 " --> pdb=" O ILE R 358 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AC4, first strand: chain 'R' and resid 473 through 474 423 hydrogen bonds defined for protein. 1116 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: 3.07 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2864 1.35 - 1.48: 2471 1.48 - 1.61: 3844 1.61 - 1.74: 0 1.74 - 1.87: 47 Bond restraints: 9226 Sorted by residual: bond pdb=" CB CYS R 379 " pdb=" SG CYS R 379 " ideal model delta sigma weight residual 1.808 1.875 -0.067 3.30e-02 9.18e+02 4.09e+00 bond pdb=" CB VAL N 48 " pdb=" CG2 VAL N 48 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.68e+00 bond pdb=" CB CYS R 432 " pdb=" SG CYS R 432 " ideal model delta sigma weight residual 1.808 1.768 0.040 3.30e-02 9.18e+02 1.48e+00 bond pdb=" C1 GLC A 1 " pdb=" O1 GLC A 1 " ideal model delta sigma weight residual 1.389 1.409 -0.020 2.00e-02 2.50e+03 9.63e-01 bond pdb=" C ILE B 133 " pdb=" N PRO B 134 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 9.00e-01 ... (remaining 9221 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 12431 2.65 - 5.31: 91 5.31 - 7.96: 3 7.96 - 10.62: 0 10.62 - 13.27: 2 Bond angle restraints: 12527 Sorted by residual: angle pdb=" N CYS R 432 " pdb=" CA CYS R 432 " pdb=" C CYS R 432 " ideal model delta sigma weight residual 107.88 119.63 -11.75 1.41e+00 5.03e-01 6.95e+01 angle pdb=" CA CYS R 432 " pdb=" CB CYS R 432 " pdb=" SG CYS R 432 " ideal model delta sigma weight residual 114.40 127.67 -13.27 2.30e+00 1.89e-01 3.33e+01 angle pdb=" C GLY R 431 " pdb=" N CYS R 432 " pdb=" CA CYS R 432 " ideal model delta sigma weight residual 122.45 118.44 4.01 1.78e+00 3.16e-01 5.07e+00 angle pdb=" N GLU B 23 " pdb=" CA GLU B 23 " pdb=" CB GLU B 23 " ideal model delta sigma weight residual 110.16 113.37 -3.21 1.48e+00 4.57e-01 4.70e+00 angle pdb=" C GLU B 173 " pdb=" N ASN B 174 " pdb=" CA ASN B 174 " ideal model delta sigma weight residual 121.54 125.58 -4.04 1.91e+00 2.74e-01 4.47e+00 ... (remaining 12522 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4970 17.94 - 35.87: 423 35.87 - 53.81: 73 53.81 - 71.75: 14 71.75 - 89.68: 11 Dihedral angle restraints: 5491 sinusoidal: 2164 harmonic: 3327 Sorted by residual: dihedral pdb=" CA GLU H 158 " pdb=" C GLU H 158 " pdb=" N PRO H 159 " pdb=" CA PRO H 159 " ideal model delta harmonic sigma weight residual 180.00 144.49 35.51 0 5.00e+00 4.00e-02 5.04e+01 dihedral pdb=" CB CYS R 379 " pdb=" SG CYS R 379 " pdb=" SG CYS R 432 " pdb=" CB CYS R 432 " ideal model delta sinusoidal sigma weight residual 93.00 34.17 58.83 1 1.00e+01 1.00e-02 4.63e+01 dihedral pdb=" CB CYS H 150 " pdb=" SG CYS H 150 " pdb=" SG CYS H 206 " pdb=" CB CYS H 206 " ideal model delta sinusoidal sigma weight residual 93.00 140.09 -47.09 1 1.00e+01 1.00e-02 3.06e+01 ... (remaining 5488 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1180 0.061 - 0.121: 177 0.121 - 0.182: 8 0.182 - 0.242: 0 0.242 - 0.303: 2 Chirality restraints: 1367 Sorted by residual: chirality pdb=" C1 GLC A 2 " pdb=" O4 GLC A 1 " pdb=" C2 GLC A 2 " pdb=" O5 GLC A 2 " both_signs ideal model delta sigma weight residual False 2.40 2.32 0.08 2.00e-02 2.50e+03 1.72e+01 chirality pdb=" C1 GLC A 1 " pdb=" C2 GLC A 1 " pdb=" O1 GLC A 1 " pdb=" O5 GLC A 1 " both_signs ideal model delta sigma weight residual False -2.04 -2.34 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CA CYS R 432 " pdb=" N CYS R 432 " pdb=" C CYS R 432 " pdb=" CB CYS R 432 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 1364 not shown) Planarity restraints: 1604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 158 " 0.076 5.00e-02 4.00e+02 1.17e-01 2.19e+01 pdb=" N PRO H 159 " -0.203 5.00e-02 4.00e+02 pdb=" CA PRO H 159 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO H 159 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER R 383 " -0.053 5.00e-02 4.00e+02 8.02e-02 1.03e+01 pdb=" N PRO R 384 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO R 384 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO R 384 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 123 " 0.050 5.00e-02 4.00e+02 7.68e-02 9.43e+00 pdb=" N PRO B 124 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO B 124 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 124 " 0.042 5.00e-02 4.00e+02 ... (remaining 1601 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 200 2.69 - 3.24: 8625 3.24 - 3.80: 14199 3.80 - 4.35: 18927 4.35 - 4.90: 31721 Nonbonded interactions: 73672 Sorted by model distance: nonbonded pdb=" OD1 ASP R 442 " pdb=" OH TYR R 451 " model vdw 2.138 3.040 nonbonded pdb=" O MET H 110 " pdb=" OH TYR L 42 " model vdw 2.140 3.040 nonbonded pdb=" ND2 ASN H 207 " pdb=" OD1 ASP H 218 " model vdw 2.145 3.120 nonbonded pdb=" OE1 GLN L 27 " pdb=" OG1 THR N 118 " model vdw 2.204 3.040 nonbonded pdb=" OD2 ASP R 398 " pdb=" OH TYR R 423 " model vdw 2.208 3.040 ... (remaining 73667 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.610 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 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 : 0.003 0.067 9226 Z= 0.204 Angle : 0.575 13.271 12527 Z= 0.302 Chirality : 0.043 0.303 1367 Planarity : 0.005 0.117 1604 Dihedral : 13.839 89.685 3344 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.21 % Allowed : 0.21 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 1.72 % 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: 0.47 (0.25), residues: 1118 helix: 0.60 (0.33), residues: 261 sheet: 0.60 (0.27), residues: 346 loop : 0.11 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 56 HIS 0.004 0.001 HIS H 35 PHE 0.020 0.002 PHE B 259 TYR 0.015 0.001 TYR R 505 ARG 0.003 0.000 ARG N 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 142 time to evaluate : 1.270 Fit side-chains REVERT: B 405 HIS cc_start: 0.8620 (t-90) cc_final: 0.8062 (t-170) REVERT: B 485 LEU cc_start: 0.8913 (tp) cc_final: 0.8315 (tp) REVERT: H 6 GLU cc_start: 0.7247 (mp0) cc_final: 0.6941 (mp0) REVERT: H 153 LYS cc_start: 0.8456 (mmtt) cc_final: 0.8255 (mmtp) outliers start: 2 outliers final: 0 residues processed: 143 average time/residue: 0.2096 time to fit residues: 42.0056 Evaluate side-chains 111 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.2980 chunk 84 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN B 204 HIS ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 143 ASN ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 9226 Z= 0.196 Angle : 0.556 14.318 12527 Z= 0.290 Chirality : 0.042 0.160 1367 Planarity : 0.005 0.100 1604 Dihedral : 4.400 33.374 1277 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.83 % Allowed : 7.35 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 1.72 % 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: 0.73 (0.25), residues: 1118 helix: 1.11 (0.32), residues: 264 sheet: 0.67 (0.27), residues: 343 loop : 0.15 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 47 HIS 0.004 0.001 HIS H 35 PHE 0.023 0.001 PHE B 510 TYR 0.034 0.001 TYR R 505 ARG 0.005 0.001 ARG L 147 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 137 time to evaluate : 1.052 Fit side-chains revert: symmetry clash REVERT: B 405 HIS cc_start: 0.8598 (t-90) cc_final: 0.8090 (t-170) REVERT: B 485 LEU cc_start: 0.8680 (tp) cc_final: 0.8408 (tp) REVERT: B 532 PHE cc_start: 0.7429 (m-80) cc_final: 0.7153 (m-80) REVERT: H 6 GLU cc_start: 0.7061 (mp0) cc_final: 0.6850 (mp0) outliers start: 8 outliers final: 6 residues processed: 141 average time/residue: 0.1953 time to fit residues: 39.5912 Evaluate side-chains 124 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 118 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain R residue 432 CYS Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.0870 chunk 31 optimal weight: 0.0980 chunk 84 optimal weight: 0.0770 chunk 69 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN B 204 HIS L 32 ASN ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 9226 Z= 0.152 Angle : 0.512 12.532 12527 Z= 0.267 Chirality : 0.041 0.141 1367 Planarity : 0.004 0.087 1604 Dihedral : 4.166 30.773 1277 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.72 % Allowed : 10.35 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 1.72 % 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: 0.87 (0.25), residues: 1118 helix: 1.29 (0.33), residues: 265 sheet: 0.63 (0.27), residues: 360 loop : 0.29 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 47 HIS 0.003 0.001 HIS H 35 PHE 0.025 0.001 PHE B 510 TYR 0.021 0.001 TYR R 505 ARG 0.003 0.000 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 145 time to evaluate : 0.994 Fit side-chains revert: symmetry clash REVERT: B 327 LYS cc_start: 0.8139 (mttt) cc_final: 0.7654 (tptt) REVERT: B 405 HIS cc_start: 0.8562 (t-90) cc_final: 0.8127 (t-170) REVERT: B 485 LEU cc_start: 0.8577 (tp) cc_final: 0.8360 (tp) REVERT: B 532 PHE cc_start: 0.7420 (m-80) cc_final: 0.6595 (m-80) REVERT: H 19 ARG cc_start: 0.8001 (ttt90) cc_final: 0.7659 (ttm-80) outliers start: 7 outliers final: 5 residues processed: 148 average time/residue: 0.1906 time to fit residues: 40.2996 Evaluate side-chains 131 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 126 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 48 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 96 optimal weight: 0.0060 chunk 29 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN B 125 ASN B 204 HIS ** B 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 9226 Z= 0.287 Angle : 0.575 12.965 12527 Z= 0.299 Chirality : 0.042 0.138 1367 Planarity : 0.004 0.074 1604 Dihedral : 4.362 30.053 1277 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.97 % Allowed : 12.94 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 1.72 % 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: 0.81 (0.25), residues: 1118 helix: 1.43 (0.33), residues: 259 sheet: 0.69 (0.27), residues: 356 loop : 0.05 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 47 HIS 0.003 0.001 HIS H 35 PHE 0.036 0.002 PHE B 510 TYR 0.020 0.002 TYR L 97 ARG 0.003 0.000 ARG N 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 128 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: B 405 HIS cc_start: 0.8631 (t-90) cc_final: 0.8194 (t-170) REVERT: H 219 LYS cc_start: 0.7574 (tppt) cc_final: 0.7284 (tppt) outliers start: 19 outliers final: 12 residues processed: 138 average time/residue: 0.1906 time to fit residues: 37.7122 Evaluate side-chains 132 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 120 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain R residue 401 VAL Chi-restraints excluded: chain R residue 432 CYS Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN B 324 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 9226 Z= 0.279 Angle : 0.575 13.153 12527 Z= 0.298 Chirality : 0.042 0.172 1367 Planarity : 0.004 0.062 1604 Dihedral : 4.475 30.475 1277 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.76 % Allowed : 14.80 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 1.72 % 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: 0.74 (0.25), residues: 1118 helix: 1.42 (0.33), residues: 260 sheet: 0.63 (0.27), residues: 360 loop : -0.01 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP N 47 HIS 0.002 0.001 HIS N 125 PHE 0.025 0.002 PHE B 510 TYR 0.020 0.002 TYR L 97 ARG 0.003 0.000 ARG N 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 1.054 Fit side-chains revert: symmetry clash REVERT: H 219 LYS cc_start: 0.7628 (tppt) cc_final: 0.7381 (tppt) REVERT: L 69 THR cc_start: 0.8039 (t) cc_final: 0.7839 (p) REVERT: R 351 TYR cc_start: 0.8029 (p90) cc_final: 0.7774 (p90) outliers start: 17 outliers final: 13 residues processed: 135 average time/residue: 0.1902 time to fit residues: 37.2326 Evaluate side-chains 130 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 117 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain R residue 401 VAL Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 63 optimal weight: 0.6980 chunk 26 optimal weight: 9.9990 chunk 108 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN ** L 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 9226 Z= 0.305 Angle : 0.597 16.403 12527 Z= 0.310 Chirality : 0.043 0.203 1367 Planarity : 0.004 0.056 1604 Dihedral : 4.565 30.627 1277 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.80 % Allowed : 15.11 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 1.72 % 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: 0.63 (0.25), residues: 1118 helix: 1.39 (0.33), residues: 260 sheet: 0.52 (0.27), residues: 355 loop : -0.08 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP N 47 HIS 0.002 0.001 HIS H 35 PHE 0.017 0.002 PHE B 510 TYR 0.021 0.002 TYR L 97 ARG 0.003 0.000 ARG N 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 124 time to evaluate : 1.057 Fit side-chains REVERT: N 93 VAL cc_start: 0.8690 (OUTLIER) cc_final: 0.8490 (m) REVERT: R 351 TYR cc_start: 0.8043 (p90) cc_final: 0.7775 (p90) outliers start: 27 outliers final: 20 residues processed: 141 average time/residue: 0.2026 time to fit residues: 40.5048 Evaluate side-chains 138 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 117 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 176 PHE Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 401 VAL Chi-restraints excluded: chain R residue 432 CYS Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 79 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 107 optimal weight: 0.0870 chunk 67 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 0.0980 chunk 66 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9226 Z= 0.165 Angle : 0.552 15.159 12527 Z= 0.285 Chirality : 0.042 0.167 1367 Planarity : 0.004 0.090 1604 Dihedral : 4.347 31.468 1277 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.28 % Allowed : 16.56 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 1.72 % 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: 0.69 (0.25), residues: 1118 helix: 1.44 (0.33), residues: 261 sheet: 0.47 (0.27), residues: 356 loop : 0.04 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP N 47 HIS 0.004 0.001 HIS H 35 PHE 0.013 0.001 PHE B 510 TYR 0.017 0.001 TYR B 100 ARG 0.002 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 123 time to evaluate : 1.035 Fit side-chains REVERT: H 47 TRP cc_start: 0.8221 (OUTLIER) cc_final: 0.7852 (t60) REVERT: L 69 THR cc_start: 0.8023 (t) cc_final: 0.7818 (p) REVERT: R 351 TYR cc_start: 0.8001 (p90) cc_final: 0.7736 (p90) outliers start: 22 outliers final: 18 residues processed: 134 average time/residue: 0.1927 time to fit residues: 36.9601 Evaluate side-chains 136 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 117 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain R residue 432 CYS Chi-restraints excluded: chain R residue 461 LEU Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 0.3980 chunk 20 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 10 optimal weight: 0.0050 chunk 84 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9226 Z= 0.185 Angle : 0.558 14.931 12527 Z= 0.286 Chirality : 0.042 0.152 1367 Planarity : 0.004 0.088 1604 Dihedral : 4.314 30.879 1277 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.28 % Allowed : 17.39 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 1.72 % 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: 0.69 (0.25), residues: 1118 helix: 1.47 (0.33), residues: 259 sheet: 0.49 (0.27), residues: 356 loop : 0.01 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 47 HIS 0.004 0.001 HIS H 35 PHE 0.012 0.001 PHE B 532 TYR 0.016 0.001 TYR B 100 ARG 0.002 0.000 ARG R 457 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 118 time to evaluate : 0.964 Fit side-chains REVERT: H 47 TRP cc_start: 0.8286 (OUTLIER) cc_final: 0.7934 (t60) REVERT: L 69 THR cc_start: 0.7997 (t) cc_final: 0.7765 (p) REVERT: R 351 TYR cc_start: 0.7953 (p90) cc_final: 0.7658 (p90) REVERT: R 357 ARG cc_start: 0.6868 (ttp-170) cc_final: 0.6524 (ttp-170) REVERT: R 481 ASN cc_start: 0.6911 (t0) cc_final: 0.6660 (t0) outliers start: 22 outliers final: 16 residues processed: 132 average time/residue: 0.1838 time to fit residues: 35.3187 Evaluate side-chains 132 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 115 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain R residue 432 CYS Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 103 optimal weight: 0.0470 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 0.0970 chunk 66 optimal weight: 0.1980 chunk 106 optimal weight: 3.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9226 Z= 0.171 Angle : 0.560 14.531 12527 Z= 0.285 Chirality : 0.042 0.156 1367 Planarity : 0.004 0.089 1604 Dihedral : 4.256 31.074 1277 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.38 % Allowed : 17.29 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 1.72 % 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: 0.69 (0.25), residues: 1118 helix: 1.54 (0.33), residues: 259 sheet: 0.49 (0.27), residues: 361 loop : -0.04 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 47 HIS 0.004 0.001 HIS H 35 PHE 0.012 0.001 PHE B 532 TYR 0.016 0.001 TYR B 100 ARG 0.002 0.000 ARG R 457 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 122 time to evaluate : 1.069 Fit side-chains REVERT: H 47 TRP cc_start: 0.8237 (OUTLIER) cc_final: 0.7849 (t60) REVERT: L 69 THR cc_start: 0.8000 (t) cc_final: 0.7764 (p) REVERT: R 351 TYR cc_start: 0.7887 (p90) cc_final: 0.7591 (p90) REVERT: R 357 ARG cc_start: 0.6879 (ttp-170) cc_final: 0.6539 (ttp-170) outliers start: 23 outliers final: 18 residues processed: 135 average time/residue: 0.1890 time to fit residues: 36.8620 Evaluate side-chains 133 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain R residue 432 CYS Chi-restraints excluded: chain R residue 461 LEU Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.0060 chunk 50 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9226 Z= 0.203 Angle : 0.577 14.472 12527 Z= 0.294 Chirality : 0.042 0.152 1367 Planarity : 0.004 0.090 1604 Dihedral : 4.320 30.630 1277 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.17 % Allowed : 17.18 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 1.72 % 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: 0.63 (0.25), residues: 1118 helix: 1.50 (0.33), residues: 259 sheet: 0.49 (0.27), residues: 361 loop : -0.12 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 47 HIS 0.004 0.001 HIS H 35 PHE 0.023 0.001 PHE B 510 TYR 0.015 0.001 TYR B 100 ARG 0.003 0.000 ARG R 457 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 122 time to evaluate : 1.046 Fit side-chains REVERT: H 47 TRP cc_start: 0.8288 (OUTLIER) cc_final: 0.7936 (t60) REVERT: L 69 THR cc_start: 0.8016 (t) cc_final: 0.7782 (p) REVERT: R 351 TYR cc_start: 0.7950 (p90) cc_final: 0.7620 (p90) outliers start: 21 outliers final: 18 residues processed: 133 average time/residue: 0.1859 time to fit residues: 35.8490 Evaluate side-chains 135 residues out of total 967 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 116 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 225 MET Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain R residue 432 CYS Chi-restraints excluded: chain R residue 461 LEU Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 88 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.196162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.169621 restraints weight = 11748.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.168735 restraints weight = 18183.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.171002 restraints weight = 13815.234| |-----------------------------------------------------------------------------| r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 9226 Z= 0.183 Angle : 0.571 14.621 12527 Z= 0.291 Chirality : 0.042 0.147 1367 Planarity : 0.004 0.088 1604 Dihedral : 4.291 30.654 1277 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.97 % Allowed : 17.39 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 1.72 % 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: 0.66 (0.25), residues: 1118 helix: 1.57 (0.33), residues: 259 sheet: 0.49 (0.27), residues: 361 loop : -0.11 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 47 HIS 0.004 0.001 HIS H 35 PHE 0.021 0.001 PHE B 510 TYR 0.017 0.001 TYR B 100 ARG 0.002 0.000 ARG R 457 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1904.07 seconds wall clock time: 35 minutes 11.75 seconds (2111.75 seconds total)