Starting phenix.real_space_refine on Thu Feb 15 05:30:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ou9_20198/02_2024/6ou9_20198.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ou9_20198/02_2024/6ou9_20198.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ou9_20198/02_2024/6ou9_20198.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ou9_20198/02_2024/6ou9_20198.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ou9_20198/02_2024/6ou9_20198.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ou9_20198/02_2024/6ou9_20198.pdb" } resolution = 3.2 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= 0.005 sd= 0.086 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 7211 2.51 5 N 1916 2.21 5 O 2085 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 26": "OE1" <-> "OE2" Residue "B GLU 31": "OE1" <-> "OE2" Residue "B PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 274": "OE1" <-> "OE2" Residue "B GLU 368": "OE1" <-> "OE2" Residue "B ARG 394": "NH1" <-> "NH2" Residue "B GLU 409": "OE1" <-> "OE2" Residue "B GLU 450": "OE1" <-> "OE2" Residue "B GLU 457": "OE1" <-> "OE2" Residue "B PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 161": "OE1" <-> "OE2" Residue "A PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A ARG 394": "NH1" <-> "NH2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "C GLU 67": "OE1" <-> "OE2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "C PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 176": "OE1" <-> "OE2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C ARG 230": "NH1" <-> "NH2" Residue "C GLU 424": "OE1" <-> "OE2" Residue "C GLU 482": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11269 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 3865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3865 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 51, 'TRANS': 455} Chain breaks: 1 Chain: "A" Number of atoms: 3703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3703 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 49, 'TRANS': 433} Chain breaks: 2 Chain: "C" Number of atoms: 3701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3701 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 49, 'TRANS': 433} Chain breaks: 2 Time building chain proxies: 6.46, per 1000 atoms: 0.57 Number of scatterers: 11269 At special positions: 0 Unit cell: (102.72, 109.14, 111.28, 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 57 16.00 O 2085 8.00 N 1916 7.00 C 7211 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.20 Conformation dependent library (CDL) restraints added in 2.1 seconds 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2710 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 19 sheets defined 8.5% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.957A pdb=" N ALA B 45 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA B 46 " --> pdb=" O THR B 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 42 through 46' Processing helix chain 'B' and resid 88 through 91 removed outlier: 3.961A pdb=" N LEU B 91 " --> pdb=" O GLY B 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 88 through 91' Processing helix chain 'B' and resid 92 through 100 removed outlier: 3.682A pdb=" N GLN B 100 " --> pdb=" O GLN B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 146 removed outlier: 3.555A pdb=" N THR B 145 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 448 through 459 removed outlier: 3.581A pdb=" N HIS B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU B 457 " --> pdb=" O SER B 453 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN B 459 " --> pdb=" O PHE B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 504 removed outlier: 3.822A pdb=" N ASN B 503 " --> pdb=" O GLY B 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 91 removed outlier: 3.955A pdb=" N LEU A 91 " --> pdb=" O GLY A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 88 through 91' Processing helix chain 'A' and resid 92 through 99 removed outlier: 3.586A pdb=" N HIS A 97 " --> pdb=" O PRO A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 147 removed outlier: 3.778A pdb=" N PHE A 147 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 448 through 459 removed outlier: 3.577A pdb=" N GLU A 457 " --> pdb=" O SER A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 504 removed outlier: 3.692A pdb=" N ASN A 503 " --> pdb=" O GLY A 500 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 504 " --> pdb=" O PRO A 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 500 through 504' Processing helix chain 'C' and resid 88 through 92 removed outlier: 4.018A pdb=" N LEU C 91 " --> pdb=" O GLY C 88 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN C 92 " --> pdb=" O PRO C 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 88 through 92' Processing helix chain 'C' and resid 94 through 99 Processing helix chain 'C' and resid 100 through 102 No H-bonds generated for 'chain 'C' and resid 100 through 102' Processing helix chain 'C' and resid 226 through 230 removed outlier: 3.715A pdb=" N THR C 229 " --> pdb=" O GLU C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 242 Processing helix chain 'C' and resid 448 through 459 removed outlier: 3.529A pdb=" N VAL C 452 " --> pdb=" O PRO C 448 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU C 457 " --> pdb=" O SER C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 504 removed outlier: 3.513A pdb=" N ASN C 503 " --> pdb=" O GLY C 500 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 63 through 71 removed outlier: 12.384A pdb=" N GLN B 64 " --> pdb=" O PRO B 211 " (cutoff:3.500A) removed outlier: 10.354A pdb=" N THR B 209 " --> pdb=" O PRO B 66 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLY B 68 " --> pdb=" O VAL B 207 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG B 206 " --> pdb=" O MET B 114 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 164 " --> pdb=" O MET B 109 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 81 through 86 removed outlier: 7.191A pdb=" N CYS B 185 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ASP B 84 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU B 183 " --> pdb=" O ASP B 84 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LYS B 124 " --> pdb=" O TYR B 188 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA B 122 " --> pdb=" O PRO B 190 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 105 through 106 removed outlier: 3.656A pdb=" N ASN B 216 " --> pdb=" O VAL B 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 251 through 255 removed outlier: 7.920A pdb=" N ILE B 251 " --> pdb=" O ASP B 432 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ASP B 432 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS B 253 " --> pdb=" O MET B 430 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 290 through 296 removed outlier: 4.238A pdb=" N LYS B 302 " --> pdb=" O PHE B 369 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLU B 368 " --> pdb=" O LYS B 355 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LYS B 355 " --> pdb=" O GLU B 368 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASP B 332 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N VAL B 386 " --> pdb=" O ASP B 332 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N HIS B 334 " --> pdb=" O ALA B 384 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 425 through 426 removed outlier: 3.960A pdb=" N PHE B 490 " --> pdb=" O TYR B 486 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA B 466 " --> pdb=" O TRP B 515 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N TRP B 515 " --> pdb=" O ALA B 466 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU B 468 " --> pdb=" O SER B 513 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 63 through 64 Processing sheet with id=AA8, first strand: chain 'A' and resid 63 through 64 removed outlier: 4.196A pdb=" N ALA A 204 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 83 through 86 removed outlier: 4.064A pdb=" N PHE A 83 " --> pdb=" O CYS A 185 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 173 through 174 Processing sheet with id=AB2, first strand: chain 'A' and resid 251 through 255 removed outlier: 6.703A pdb=" N MET A 430 " --> pdb=" O ASN A 252 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N MET A 254 " --> pdb=" O TYR A 428 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TYR A 428 " --> pdb=" O MET A 254 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 349 through 354 removed outlier: 3.700A pdb=" N TRP A 385 " --> pdb=" O HIS A 334 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N SER A 336 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEU A 383 " --> pdb=" O SER A 336 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N PHE A 338 " --> pdb=" O GLY A 381 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N GLY A 381 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS A 302 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 369 " --> pdb=" O LYS A 302 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 425 through 426 removed outlier: 4.083A pdb=" N PHE A 490 " --> pdb=" O TYR A 486 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY A 481 " --> pdb=" O TYR A 471 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA A 466 " --> pdb=" O TRP A 515 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N TRP A 515 " --> pdb=" O ALA A 466 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU A 468 " --> pdb=" O SER A 513 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 63 through 72 removed outlier: 12.388A pdb=" N GLN C 64 " --> pdb=" O PRO C 211 " (cutoff:3.500A) removed outlier: 10.745A pdb=" N THR C 209 " --> pdb=" O PRO C 66 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N GLY C 68 " --> pdb=" O VAL C 207 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 81 through 86 removed outlier: 6.983A pdb=" N CYS C 185 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ASP C 84 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU C 183 " --> pdb=" O ASP C 84 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR C 188 " --> pdb=" O LYS C 124 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LYS C 124 " --> pdb=" O TYR C 188 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA C 122 " --> pdb=" O PRO C 190 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 173 through 174 Processing sheet with id=AB8, first strand: chain 'C' and resid 253 through 255 removed outlier: 4.204A pdb=" N LYS C 253 " --> pdb=" O MET C 430 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 290 through 297 removed outlier: 4.453A pdb=" N LYS C 302 " --> pdb=" O PHE C 369 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLU C 368 " --> pdb=" O LYS C 355 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LYS C 355 " --> pdb=" O GLU C 368 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TRP C 385 " --> pdb=" O HIS C 334 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N SER C 336 " --> pdb=" O LEU C 383 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N LEU C 383 " --> pdb=" O SER C 336 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N PHE C 338 " --> pdb=" O GLY C 381 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLY C 381 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 425 through 426 removed outlier: 6.484A pdb=" N TYR C 471 " --> pdb=" O LEU C 480 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLU C 482 " --> pdb=" O LEU C 469 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU C 469 " --> pdb=" O GLU C 482 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LYS C 484 " --> pdb=" O ALA C 467 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA C 467 " --> pdb=" O LYS C 484 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA C 466 " --> pdb=" O TRP C 515 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N TRP C 515 " --> pdb=" O ALA C 466 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LEU C 468 " --> pdb=" O SER C 513 " (cutoff:3.500A) 248 hydrogen bonds defined for protein. 624 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: 3.46 Time building geometry restraints manager: 4.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3676 1.34 - 1.45: 1753 1.45 - 1.57: 6077 1.57 - 1.69: 0 1.69 - 1.80: 90 Bond restraints: 11596 Sorted by residual: bond pdb=" N ARG C 178 " pdb=" CA ARG C 178 " ideal model delta sigma weight residual 1.456 1.427 0.029 1.48e-02 4.57e+03 3.75e+00 bond pdb=" CB VAL C 106 " pdb=" CG1 VAL C 106 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.21e+00 bond pdb=" C ILE C 400 " pdb=" N PRO C 401 " ideal model delta sigma weight residual 1.330 1.345 -0.015 1.25e-02 6.40e+03 1.36e+00 bond pdb=" C ALA C 65 " pdb=" N PRO C 66 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.33e+00 bond pdb=" C SER B 73 " pdb=" N PRO B 74 " ideal model delta sigma weight residual 1.334 1.343 -0.010 8.40e-03 1.42e+04 1.33e+00 ... (remaining 11591 not shown) Histogram of bond angle deviations from ideal: 98.96 - 105.97: 569 105.97 - 112.98: 6124 112.98 - 119.98: 3760 119.98 - 126.99: 5228 126.99 - 134.00: 200 Bond angle restraints: 15881 Sorted by residual: angle pdb=" C VAL B 221 " pdb=" CA VAL B 221 " pdb=" CB VAL B 221 " ideal model delta sigma weight residual 109.33 115.00 -5.67 9.80e-01 1.04e+00 3.34e+01 angle pdb=" N VAL B 340 " pdb=" CA VAL B 340 " pdb=" C VAL B 340 " ideal model delta sigma weight residual 113.07 106.72 6.35 1.37e+00 5.33e-01 2.15e+01 angle pdb=" N VAL B 221 " pdb=" CA VAL B 221 " pdb=" C VAL B 221 " ideal model delta sigma weight residual 109.19 105.90 3.29 8.20e-01 1.49e+00 1.61e+01 angle pdb=" CA VAL B 221 " pdb=" C VAL B 221 " pdb=" N PRO B 222 " ideal model delta sigma weight residual 116.57 119.95 -3.38 9.80e-01 1.04e+00 1.19e+01 angle pdb=" N ARG C 178 " pdb=" CA ARG C 178 " pdb=" C ARG C 178 " ideal model delta sigma weight residual 107.95 100.88 7.07 2.14e+00 2.18e-01 1.09e+01 ... (remaining 15876 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 6324 17.44 - 34.89: 463 34.89 - 52.33: 89 52.33 - 69.77: 12 69.77 - 87.22: 7 Dihedral angle restraints: 6895 sinusoidal: 2693 harmonic: 4202 Sorted by residual: dihedral pdb=" CA PHE C 217 " pdb=" C PHE C 217 " pdb=" N LEU C 218 " pdb=" CA LEU C 218 " ideal model delta harmonic sigma weight residual 180.00 -155.74 -24.26 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA VAL C 340 " pdb=" C VAL C 340 " pdb=" N ASP C 341 " pdb=" CA ASP C 341 " ideal model delta harmonic sigma weight residual 180.00 -156.37 -23.63 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA ARG A 182 " pdb=" C ARG A 182 " pdb=" N LEU A 183 " pdb=" CA LEU A 183 " ideal model delta harmonic sigma weight residual 180.00 159.90 20.10 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 6892 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 954 0.035 - 0.070: 504 0.070 - 0.104: 180 0.104 - 0.139: 122 0.139 - 0.174: 23 Chirality restraints: 1783 Sorted by residual: chirality pdb=" CB THR A 497 " pdb=" CA THR A 497 " pdb=" OG1 THR A 497 " pdb=" CG2 THR A 497 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.57e-01 chirality pdb=" CA VAL C 256 " pdb=" N VAL C 256 " pdb=" C VAL C 256 " pdb=" CB VAL C 256 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.17 2.00e-01 2.50e+01 7.56e-01 chirality pdb=" CB ILE B 126 " pdb=" CA ILE B 126 " pdb=" CG1 ILE B 126 " pdb=" CG2 ILE B 126 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.52e-01 ... (remaining 1780 not shown) Planarity restraints: 2112 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 212 " 0.055 5.00e-02 4.00e+02 8.39e-02 1.13e+01 pdb=" N PRO A 213 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 213 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 213 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 212 " -0.053 5.00e-02 4.00e+02 8.05e-02 1.04e+01 pdb=" N PRO B 213 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO B 213 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 213 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 212 " 0.049 5.00e-02 4.00e+02 7.37e-02 8.69e+00 pdb=" N PRO C 213 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO C 213 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 213 " 0.041 5.00e-02 4.00e+02 ... (remaining 2109 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 106 2.63 - 3.20: 8951 3.20 - 3.77: 15624 3.77 - 4.33: 22055 4.33 - 4.90: 37821 Nonbonded interactions: 84557 Sorted by model distance: nonbonded pdb=" NH2 ARG C 394 " pdb=" OD1 ASN C 439 " model vdw 2.067 2.520 nonbonded pdb=" NZ LYS A 294 " pdb=" OD2 ASP A 378 " model vdw 2.265 2.520 nonbonded pdb=" CE LYS A 294 " pdb=" OD2 ASP A 378 " model vdw 2.300 3.440 nonbonded pdb=" O ASN C 108 " pdb=" OG SER C 212 " model vdw 2.310 2.440 nonbonded pdb=" OG SER C 319 " pdb=" O ALA C 321 " model vdw 2.330 2.440 ... (remaining 84552 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 404 or resid 412 through 526)) selection = (chain 'B' and (resid 33 through 404 or resid 412 through 526)) selection = (chain 'C' and (resid 33 through 193 or resid 200 through 404 or resid 412 throu \ gh 526)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.030 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: 0.890 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 32.320 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 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 : 0.006 0.055 11596 Z= 0.384 Angle : 0.753 8.822 15881 Z= 0.430 Chirality : 0.054 0.174 1783 Planarity : 0.009 0.084 2112 Dihedral : 12.958 87.217 4185 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % 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: -3.26 (0.18), residues: 1457 helix: -4.17 (0.26), residues: 71 sheet: -1.49 (0.24), residues: 387 loop : -2.44 (0.16), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 385 HIS 0.003 0.001 HIS C 470 PHE 0.027 0.002 PHE C 83 TYR 0.009 0.002 TYR A 102 ARG 0.006 0.000 ARG C 518 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 305 time to evaluate : 1.263 Fit side-chains REVERT: B 57 TRP cc_start: 0.8875 (m100) cc_final: 0.8604 (m100) REVERT: B 192 ARG cc_start: 0.7941 (mmt-90) cc_final: 0.7414 (mtt180) REVERT: B 308 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8405 (mm-30) REVERT: B 430 MET cc_start: 0.8966 (mmm) cc_final: 0.8563 (mmm) REVERT: A 252 ASN cc_start: 0.8622 (t0) cc_final: 0.8374 (t0) REVERT: A 396 ASP cc_start: 0.8761 (t0) cc_final: 0.8511 (t0) REVERT: A 458 GLN cc_start: 0.8465 (tt0) cc_final: 0.8223 (tt0) REVERT: A 478 ARG cc_start: 0.8080 (mtp180) cc_final: 0.7860 (mmm160) REVERT: C 290 ARG cc_start: 0.8624 (mmm-85) cc_final: 0.8330 (mmm-85) REVERT: C 338 PHE cc_start: 0.8077 (p90) cc_final: 0.7767 (p90) REVERT: C 349 MET cc_start: 0.8446 (mmm) cc_final: 0.8209 (mmm) REVERT: C 457 GLU cc_start: 0.7006 (tp30) cc_final: 0.6790 (tp30) REVERT: C 465 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7651 (mt-10) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.2219 time to fit residues: 95.9390 Evaluate side-chains 261 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 ASN B 315 HIS ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 60 ASN A 108 ASN A 357 ASN ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 ASN C 76 ASN C 86 HIS C 173 HIS C 479 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11596 Z= 0.217 Angle : 0.546 7.020 15881 Z= 0.274 Chirality : 0.046 0.159 1783 Planarity : 0.006 0.057 2112 Dihedral : 4.758 22.285 1546 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.36 % Allowed : 7.90 % Favored : 90.74 % 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: -2.53 (0.19), residues: 1457 helix: -3.26 (0.38), residues: 79 sheet: -1.15 (0.24), residues: 399 loop : -1.86 (0.18), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 385 HIS 0.006 0.001 HIS C 86 PHE 0.018 0.001 PHE C 83 TYR 0.009 0.001 TYR C 520 ARG 0.003 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 291 time to evaluate : 1.342 Fit side-chains REVERT: B 57 TRP cc_start: 0.8883 (m100) cc_final: 0.8621 (m100) REVERT: B 192 ARG cc_start: 0.7900 (mmt-90) cc_final: 0.7374 (mtt180) REVERT: B 237 ILE cc_start: 0.9292 (mt) cc_final: 0.9005 (mm) REVERT: B 294 LYS cc_start: 0.8370 (mtmm) cc_final: 0.7974 (ttmm) REVERT: B 430 MET cc_start: 0.9021 (mmm) cc_final: 0.8820 (mmm) REVERT: A 236 ASN cc_start: 0.8919 (t0) cc_final: 0.8719 (t0) REVERT: A 252 ASN cc_start: 0.8729 (t0) cc_final: 0.8092 (t0) REVERT: A 396 ASP cc_start: 0.8777 (t0) cc_final: 0.8496 (t0) REVERT: C 236 ASN cc_start: 0.8644 (t0) cc_final: 0.8353 (t0) REVERT: C 287 GLN cc_start: 0.8913 (mt0) cc_final: 0.8554 (mt0) REVERT: C 290 ARG cc_start: 0.8594 (mmm-85) cc_final: 0.8390 (mmm-85) REVERT: C 465 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7595 (mt-10) REVERT: C 479 ASN cc_start: 0.8335 (OUTLIER) cc_final: 0.7787 (t0) outliers start: 17 outliers final: 12 residues processed: 298 average time/residue: 0.2183 time to fit residues: 93.4708 Evaluate side-chains 284 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 271 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 315 HIS Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 514 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 132 optimal weight: 40.0000 chunk 143 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 131 optimal weight: 20.0000 chunk 45 optimal weight: 9.9990 chunk 106 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 60 ASN C 86 HIS ** C 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 11596 Z= 0.299 Angle : 0.553 8.248 15881 Z= 0.274 Chirality : 0.047 0.157 1783 Planarity : 0.005 0.053 2112 Dihedral : 4.607 21.566 1546 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.60 % Allowed : 11.41 % Favored : 86.99 % 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: -2.17 (0.20), residues: 1457 helix: -2.84 (0.43), residues: 79 sheet: -0.92 (0.24), residues: 399 loop : -1.61 (0.18), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 385 HIS 0.015 0.001 HIS B 315 PHE 0.017 0.001 PHE C 83 TYR 0.009 0.001 TYR C 520 ARG 0.003 0.000 ARG C 478 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 271 time to evaluate : 1.288 Fit side-chains REVERT: B 57 TRP cc_start: 0.8892 (m100) cc_final: 0.8613 (m100) REVERT: B 192 ARG cc_start: 0.7884 (mmt-90) cc_final: 0.7371 (mtt180) REVERT: B 237 ILE cc_start: 0.9329 (mt) cc_final: 0.9027 (mm) REVERT: B 294 LYS cc_start: 0.8365 (mtmm) cc_final: 0.8037 (ttmm) REVERT: A 252 ASN cc_start: 0.8749 (t0) cc_final: 0.8255 (t0) REVERT: A 396 ASP cc_start: 0.8781 (t0) cc_final: 0.8495 (t0) REVERT: C 236 ASN cc_start: 0.8721 (t0) cc_final: 0.8452 (t0) REVERT: C 287 GLN cc_start: 0.8940 (mt0) cc_final: 0.8618 (mt0) REVERT: C 302 LYS cc_start: 0.7991 (ttmm) cc_final: 0.7643 (tppt) outliers start: 20 outliers final: 18 residues processed: 278 average time/residue: 0.2271 time to fit residues: 89.8189 Evaluate side-chains 277 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 259 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 315 HIS Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 514 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 6.9990 chunk 99 optimal weight: 0.0010 chunk 68 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 89 optimal weight: 8.9990 chunk 133 optimal weight: 0.8980 chunk 141 optimal weight: 20.0000 chunk 69 optimal weight: 7.9990 chunk 126 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 overall best weight: 2.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 ASN ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 60 ASN C 90 HIS C 479 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11596 Z= 0.155 Angle : 0.491 7.506 15881 Z= 0.240 Chirality : 0.045 0.155 1783 Planarity : 0.005 0.049 2112 Dihedral : 4.194 20.077 1546 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.68 % Allowed : 13.17 % Favored : 85.16 % 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: -1.71 (0.20), residues: 1457 helix: -2.42 (0.46), residues: 79 sheet: -0.54 (0.25), residues: 386 loop : -1.32 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 385 HIS 0.006 0.001 HIS C 86 PHE 0.014 0.001 PHE C 83 TYR 0.009 0.001 TYR C 520 ARG 0.007 0.000 ARG C 290 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 277 time to evaluate : 1.259 Fit side-chains REVERT: B 57 TRP cc_start: 0.8838 (m100) cc_final: 0.8587 (m100) REVERT: B 192 ARG cc_start: 0.7800 (mmt-90) cc_final: 0.7256 (mtt180) REVERT: B 237 ILE cc_start: 0.9336 (mt) cc_final: 0.9027 (mm) REVERT: A 252 ASN cc_start: 0.8748 (t0) cc_final: 0.8107 (t0) REVERT: A 396 ASP cc_start: 0.8733 (t0) cc_final: 0.8513 (t0) REVERT: A 518 ARG cc_start: 0.7824 (ptp-110) cc_final: 0.7326 (ptm-80) REVERT: C 287 GLN cc_start: 0.8892 (mt0) cc_final: 0.8599 (mt0) outliers start: 21 outliers final: 15 residues processed: 282 average time/residue: 0.2194 time to fit residues: 88.7351 Evaluate side-chains 280 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 265 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 254 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 7.9990 chunk 80 optimal weight: 0.5980 chunk 2 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 120 optimal weight: 20.0000 chunk 97 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 72 optimal weight: 5.9990 chunk 126 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 overall best weight: 6.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 315 HIS ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 GLN A 60 ASN A 118 ASN A 236 ASN C 86 HIS C 236 ASN C 470 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 11596 Z= 0.364 Angle : 0.566 9.051 15881 Z= 0.279 Chirality : 0.047 0.159 1783 Planarity : 0.005 0.046 2112 Dihedral : 4.468 20.409 1546 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.87 % Allowed : 13.49 % Favored : 83.64 % 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: -1.65 (0.21), residues: 1457 helix: -2.36 (0.46), residues: 79 sheet: -0.54 (0.25), residues: 389 loop : -1.27 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 105 HIS 0.005 0.001 HIS A 412 PHE 0.017 0.001 PHE C 83 TYR 0.009 0.001 TYR A 471 ARG 0.005 0.000 ARG C 290 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 258 time to evaluate : 1.314 Fit side-chains REVERT: B 57 TRP cc_start: 0.8873 (m100) cc_final: 0.8600 (m100) REVERT: B 192 ARG cc_start: 0.7856 (mmt-90) cc_final: 0.7364 (mtt180) REVERT: B 294 LYS cc_start: 0.8363 (mtmm) cc_final: 0.8083 (ttmm) REVERT: B 422 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.7842 (t80) REVERT: A 252 ASN cc_start: 0.8768 (t0) cc_final: 0.8260 (t0) outliers start: 36 outliers final: 26 residues processed: 271 average time/residue: 0.2230 time to fit residues: 86.2475 Evaluate side-chains 279 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 252 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 99 SER Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 315 HIS Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 210 CYS Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 355 LYS Chi-restraints excluded: chain C residue 514 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 9.9990 chunk 127 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 141 optimal weight: 20.0000 chunk 117 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 11 optimal weight: 0.0270 chunk 46 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 overall best weight: 3.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 ASN B 315 HIS ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 ASN A 356 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11596 Z= 0.229 Angle : 0.520 8.290 15881 Z= 0.255 Chirality : 0.046 0.153 1783 Planarity : 0.005 0.044 2112 Dihedral : 4.300 19.923 1546 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.63 % Allowed : 13.57 % Favored : 83.80 % 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: -1.46 (0.21), residues: 1457 helix: -2.14 (0.47), residues: 79 sheet: -0.49 (0.25), residues: 399 loop : -1.10 (0.19), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 385 HIS 0.011 0.001 HIS B 315 PHE 0.015 0.001 PHE C 83 TYR 0.006 0.001 TYR A 471 ARG 0.004 0.000 ARG C 290 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 262 time to evaluate : 1.338 Fit side-chains revert: symmetry clash REVERT: B 57 TRP cc_start: 0.8860 (m100) cc_final: 0.8578 (m100) REVERT: B 192 ARG cc_start: 0.7765 (mmt-90) cc_final: 0.7258 (mtt180) REVERT: B 422 PHE cc_start: 0.8375 (OUTLIER) cc_final: 0.7810 (t80) REVERT: B 430 MET cc_start: 0.8775 (mmm) cc_final: 0.8552 (mmm) REVERT: A 252 ASN cc_start: 0.8746 (t0) cc_final: 0.8096 (t0) REVERT: C 287 GLN cc_start: 0.8946 (mt0) cc_final: 0.8663 (mt0) outliers start: 33 outliers final: 26 residues processed: 273 average time/residue: 0.2222 time to fit residues: 87.2747 Evaluate side-chains 277 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 250 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 315 HIS Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 355 LYS Chi-restraints excluded: chain C residue 514 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 0.0270 chunk 15 optimal weight: 0.0770 chunk 80 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 79 optimal weight: 20.0000 chunk 118 optimal weight: 8.9990 chunk 78 optimal weight: 0.1980 chunk 140 optimal weight: 20.0000 chunk 88 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 overall best weight: 2.0600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11596 Z= 0.157 Angle : 0.502 8.651 15881 Z= 0.244 Chirality : 0.045 0.152 1783 Planarity : 0.005 0.043 2112 Dihedral : 4.110 18.987 1546 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.08 % Allowed : 14.84 % Favored : 83.08 % 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: -1.21 (0.21), residues: 1457 helix: -1.79 (0.50), residues: 79 sheet: -0.31 (0.25), residues: 391 loop : -0.94 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 385 HIS 0.006 0.001 HIS C 86 PHE 0.013 0.001 PHE C 83 TYR 0.006 0.001 TYR C 471 ARG 0.004 0.000 ARG C 290 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 252 time to evaluate : 1.305 Fit side-chains revert: symmetry clash REVERT: B 57 TRP cc_start: 0.8860 (m100) cc_final: 0.8612 (m100) REVERT: B 192 ARG cc_start: 0.7758 (mmt-90) cc_final: 0.7248 (mtt180) REVERT: B 422 PHE cc_start: 0.8187 (OUTLIER) cc_final: 0.7670 (t80) REVERT: A 252 ASN cc_start: 0.8738 (t0) cc_final: 0.8093 (t0) REVERT: C 287 GLN cc_start: 0.8935 (mt0) cc_final: 0.8669 (mt0) REVERT: C 302 LYS cc_start: 0.7871 (ttmm) cc_final: 0.7603 (tppt) REVERT: C 349 MET cc_start: 0.8384 (mmm) cc_final: 0.8099 (mmm) outliers start: 26 outliers final: 22 residues processed: 261 average time/residue: 0.2182 time to fit residues: 81.4543 Evaluate side-chains 280 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 257 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 236 ASN Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 514 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 40.0000 chunk 56 optimal weight: 8.9990 chunk 84 optimal weight: 20.0000 chunk 42 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 69 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 110 optimal weight: 20.0000 chunk 128 optimal weight: 0.6980 overall best weight: 7.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 HIS C 503 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 11596 Z= 0.404 Angle : 0.587 9.239 15881 Z= 0.288 Chirality : 0.048 0.204 1783 Planarity : 0.005 0.042 2112 Dihedral : 4.421 19.601 1546 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.95 % Allowed : 14.21 % Favored : 82.84 % 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: -1.30 (0.21), residues: 1457 helix: -1.66 (0.51), residues: 79 sheet: -0.32 (0.26), residues: 391 loop : -1.05 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 333 HIS 0.006 0.001 HIS A 412 PHE 0.016 0.002 PHE C 83 TYR 0.010 0.001 TYR A 471 ARG 0.004 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 260 time to evaluate : 1.293 Fit side-chains REVERT: B 57 TRP cc_start: 0.8884 (m100) cc_final: 0.8599 (m100) REVERT: B 192 ARG cc_start: 0.7787 (mmt-90) cc_final: 0.7279 (mtt180) REVERT: B 237 ILE cc_start: 0.9214 (mt) cc_final: 0.8930 (mm) REVERT: B 259 ASP cc_start: 0.7947 (t0) cc_final: 0.7620 (t0) REVERT: B 422 PHE cc_start: 0.8225 (OUTLIER) cc_final: 0.7715 (t80) REVERT: B 430 MET cc_start: 0.8783 (mmm) cc_final: 0.8527 (mmm) REVERT: A 69 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7961 (mm-30) REVERT: C 108 ASN cc_start: 0.8859 (OUTLIER) cc_final: 0.8656 (m-40) outliers start: 37 outliers final: 26 residues processed: 274 average time/residue: 0.2266 time to fit residues: 88.2571 Evaluate side-chains 284 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 255 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 210 CYS Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 355 LYS Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 514 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 20.0000 chunk 122 optimal weight: 0.0570 chunk 131 optimal weight: 20.0000 chunk 78 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 130 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 ASN ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11596 Z= 0.188 Angle : 0.510 7.511 15881 Z= 0.249 Chirality : 0.046 0.150 1783 Planarity : 0.005 0.041 2112 Dihedral : 4.136 18.549 1546 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.55 % Allowed : 14.92 % Favored : 82.52 % 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: -1.06 (0.21), residues: 1457 helix: -1.35 (0.54), residues: 79 sheet: -0.20 (0.26), residues: 391 loop : -0.87 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 385 HIS 0.006 0.001 HIS C 86 PHE 0.013 0.001 PHE C 83 TYR 0.010 0.001 TYR C 520 ARG 0.007 0.000 ARG C 290 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 258 time to evaluate : 1.168 Fit side-chains REVERT: B 57 TRP cc_start: 0.8868 (m100) cc_final: 0.8586 (m100) REVERT: B 192 ARG cc_start: 0.7762 (mmt-90) cc_final: 0.7247 (mtt180) REVERT: B 422 PHE cc_start: 0.8176 (OUTLIER) cc_final: 0.7674 (t80) REVERT: A 252 ASN cc_start: 0.8747 (t0) cc_final: 0.8063 (t0) REVERT: A 518 ARG cc_start: 0.7877 (ptp-110) cc_final: 0.7374 (ptm-80) REVERT: C 287 GLN cc_start: 0.9009 (mt0) cc_final: 0.8730 (mt0) REVERT: C 294 LYS cc_start: 0.7803 (mmmm) cc_final: 0.7580 (mmmm) REVERT: C 302 LYS cc_start: 0.7918 (ttmm) cc_final: 0.7652 (tppt) outliers start: 32 outliers final: 28 residues processed: 268 average time/residue: 0.2398 time to fit residues: 92.4499 Evaluate side-chains 284 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 255 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 315 HIS Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 236 ASN Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 514 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 7.9990 chunk 84 optimal weight: 20.0000 chunk 65 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 145 optimal weight: 0.2980 chunk 133 optimal weight: 20.0000 chunk 115 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 chunk 71 optimal weight: 0.6980 chunk 92 optimal weight: 7.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11596 Z= 0.221 Angle : 0.521 7.341 15881 Z= 0.254 Chirality : 0.046 0.151 1783 Planarity : 0.005 0.041 2112 Dihedral : 4.121 18.677 1546 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.71 % Allowed : 14.76 % Favored : 82.52 % 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: -0.99 (0.21), residues: 1457 helix: -1.27 (0.54), residues: 79 sheet: -0.16 (0.26), residues: 391 loop : -0.81 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 385 HIS 0.006 0.001 HIS C 86 PHE 0.013 0.001 PHE C 83 TYR 0.010 0.001 TYR C 520 ARG 0.007 0.000 ARG C 290 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 254 time to evaluate : 1.345 Fit side-chains REVERT: B 57 TRP cc_start: 0.8872 (m100) cc_final: 0.8590 (m100) REVERT: B 192 ARG cc_start: 0.7769 (mmt-90) cc_final: 0.7256 (mtt180) REVERT: B 422 PHE cc_start: 0.8177 (OUTLIER) cc_final: 0.7680 (t80) REVERT: A 80 ASP cc_start: 0.7896 (m-30) cc_final: 0.7521 (m-30) REVERT: A 518 ARG cc_start: 0.7882 (ptp-110) cc_final: 0.7378 (ptm-80) REVERT: C 287 GLN cc_start: 0.9021 (mt0) cc_final: 0.8744 (mt0) REVERT: C 302 LYS cc_start: 0.7944 (ttmm) cc_final: 0.7680 (tppt) outliers start: 34 outliers final: 30 residues processed: 266 average time/residue: 0.2280 time to fit residues: 86.6439 Evaluate side-chains 286 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 255 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 128 CYS Chi-restraints excluded: chain B residue 186 MET Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 236 ASN Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 210 CYS Chi-restraints excluded: chain C residue 514 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 5.9990 chunk 35 optimal weight: 20.0000 chunk 106 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 GLN ** 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 = 0.3236 r_free = 0.3236 target = 0.112634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.088178 restraints weight = 16266.826| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 2.58 r_work: 0.2675 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2536 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11596 Z= 0.276 Angle : 0.537 7.487 15881 Z= 0.262 Chirality : 0.047 0.168 1783 Planarity : 0.005 0.041 2112 Dihedral : 4.175 18.892 1546 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.71 % Allowed : 14.68 % Favored : 82.60 % 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: -1.00 (0.21), residues: 1457 helix: -1.30 (0.54), residues: 79 sheet: -0.17 (0.26), residues: 391 loop : -0.83 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 385 HIS 0.006 0.001 HIS C 86 PHE 0.014 0.001 PHE C 172 TYR 0.009 0.001 TYR C 520 ARG 0.007 0.000 ARG C 290 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2649.82 seconds wall clock time: 48 minutes 26.84 seconds (2906.84 seconds total)