Starting phenix.real_space_refine (version: dev) on Mon Feb 20 03:35:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ou9_20198/02_2023/6ou9_20198.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ou9_20198/02_2023/6ou9_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_2023/6ou9_20198.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ou9_20198/02_2023/6ou9_20198.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ou9_20198/02_2023/6ou9_20198.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ou9_20198/02_2023/6ou9_20198.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 6.36, per 1000 atoms: 0.56 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: 4.29 Conformation dependent library (CDL) restraints added in 1.7 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: 0.65 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: 3.12 Time building geometry restraints manager: 4.64 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 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. 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: 0.050 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: 1.350 Check model and map are aligned: 0.180 Process input model: 30.480 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.110 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 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 % 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 *********************** 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 : 1.273 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.2297 time to fit residues: 99.2460 Evaluate side-chains 259 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 1.359 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8630 ------------------------------------------------------------------------------- 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: 2.9990 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: 0.9980 chunk 85 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 442 GLN ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 ASN C 76 ASN C 86 HIS C 90 HIS C 173 HIS C 479 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 11596 Z= 0.203 Angle : 0.545 6.905 15881 Z= 0.273 Chirality : 0.046 0.159 1783 Planarity : 0.006 0.058 2112 Dihedral : 4.757 22.265 1546 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer Outliers : 1.44 % 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: -2.54 (0.19), residues: 1457 helix: -3.27 (0.38), residues: 79 sheet: -1.16 (0.24), residues: 399 loop : -1.86 (0.17), residues: 979 *********************** 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 307 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 289 time to evaluate : 1.393 Fit side-chains outliers start: 18 outliers final: 13 residues processed: 296 average time/residue: 0.2223 time to fit residues: 95.0263 Evaluate side-chains 280 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 267 time to evaluate : 1.352 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1266 time to fit residues: 4.9802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 110 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 36 optimal weight: 0.0060 chunk 132 optimal weight: 20.0000 chunk 143 optimal weight: 4.9990 chunk 118 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 overall best weight: 2.6004 ------------------------------------------------------------------------------- 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 A 236 ASN A 458 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 11596 Z= 0.179 Angle : 0.508 6.903 15881 Z= 0.250 Chirality : 0.045 0.157 1783 Planarity : 0.005 0.052 2112 Dihedral : 4.306 20.744 1546 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer Outliers : 0.80 % 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: -1.99 (0.20), residues: 1457 helix: -2.70 (0.44), residues: 79 sheet: -0.81 (0.24), residues: 399 loop : -1.47 (0.18), residues: 979 *********************** 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: 10 poor density : 281 time to evaluate : 1.408 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 284 average time/residue: 0.2364 time to fit residues: 96.6184 Evaluate side-chains 271 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 266 time to evaluate : 1.502 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1120 time to fit residues: 2.7200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 68 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 133 optimal weight: 10.0000 chunk 141 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 126 optimal weight: 9.9990 chunk 38 optimal weight: 20.0000 overall best weight: 3.2986 ------------------------------------------------------------------------------- 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 A 118 ASN A 236 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 11596 Z= 0.207 Angle : 0.505 7.425 15881 Z= 0.247 Chirality : 0.045 0.153 1783 Planarity : 0.005 0.047 2112 Dihedral : 4.197 20.151 1546 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer Outliers : 1.28 % 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: -1.66 (0.20), residues: 1457 helix: -2.40 (0.46), residues: 79 sheet: -0.51 (0.25), residues: 393 loop : -1.28 (0.19), residues: 985 *********************** 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 284 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 268 time to evaluate : 1.403 Fit side-chains outliers start: 16 outliers final: 10 residues processed: 270 average time/residue: 0.2335 time to fit residues: 90.3131 Evaluate side-chains 271 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 261 time to evaluate : 1.458 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1126 time to fit residues: 3.9487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 58 optimal weight: 0.4980 chunk 120 optimal weight: 20.0000 chunk 97 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 72 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 overall best weight: 5.8988 ------------------------------------------------------------------------------- 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 A 236 ASN ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 11596 Z= 0.333 Angle : 0.551 8.684 15881 Z= 0.271 Chirality : 0.047 0.157 1783 Planarity : 0.005 0.045 2112 Dihedral : 4.391 20.004 1546 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer Outliers : 1.36 % 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: -1.56 (0.21), residues: 1457 helix: -2.35 (0.46), residues: 79 sheet: -0.47 (0.25), residues: 396 loop : -1.21 (0.19), residues: 982 *********************** 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 278 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 261 time to evaluate : 1.452 Fit side-chains outliers start: 17 outliers final: 13 residues processed: 265 average time/residue: 0.2367 time to fit residues: 89.3839 Evaluate side-chains 263 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 250 time to evaluate : 1.327 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1043 time to fit residues: 4.3370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 10.0000 chunk 127 optimal weight: 20.0000 chunk 27 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 141 optimal weight: 20.0000 chunk 117 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 A 458 GLN C 75 ASN C 236 ASN C 503 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 11596 Z= 0.354 Angle : 0.566 9.569 15881 Z= 0.277 Chirality : 0.048 0.154 1783 Planarity : 0.005 0.044 2112 Dihedral : 4.479 20.209 1546 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer Outliers : 1.36 % 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: -1.52 (0.21), residues: 1457 helix: -2.25 (0.46), residues: 79 sheet: -0.50 (0.25), residues: 406 loop : -1.15 (0.19), residues: 972 *********************** 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 268 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 251 time to evaluate : 1.282 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 261 average time/residue: 0.2315 time to fit residues: 86.4861 Evaluate side-chains 252 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 243 time to evaluate : 1.339 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1374 time to fit residues: 3.9262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 0.2980 chunk 15 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 140 optimal weight: 20.0000 chunk 88 optimal weight: 7.9990 chunk 85 optimal weight: 0.1980 chunk 64 optimal weight: 10.0000 overall best weight: 3.2986 ------------------------------------------------------------------------------- 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 356 GLN C 470 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 11596 Z= 0.204 Angle : 0.515 7.863 15881 Z= 0.251 Chirality : 0.046 0.150 1783 Planarity : 0.005 0.043 2112 Dihedral : 4.220 19.478 1546 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer Outliers : 0.40 % 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: -1.25 (0.21), residues: 1457 helix: -1.84 (0.49), residues: 79 sheet: -0.28 (0.26), residues: 389 loop : -1.00 (0.19), residues: 989 *********************** 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 268 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 263 time to evaluate : 1.382 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 265 average time/residue: 0.2352 time to fit residues: 88.6378 Evaluate side-chains 261 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 258 time to evaluate : 1.344 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1389 time to fit residues: 2.5050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 0.0050 chunk 56 optimal weight: 7.9990 chunk 84 optimal weight: 20.0000 chunk 42 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 13 optimal weight: 0.3980 chunk 110 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 overall best weight: 3.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 442 GLN ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 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 : 0.003 0.044 11596 Z= 0.215 Angle : 0.519 8.964 15881 Z= 0.253 Chirality : 0.046 0.150 1783 Planarity : 0.005 0.043 2112 Dihedral : 4.146 19.003 1546 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer Outliers : 0.88 % 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: -1.08 (0.21), residues: 1457 helix: -1.49 (0.52), residues: 79 sheet: -0.20 (0.26), residues: 389 loop : -0.88 (0.19), residues: 989 *********************** 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 274 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 263 time to evaluate : 1.443 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 266 average time/residue: 0.2457 time to fit residues: 92.8701 Evaluate side-chains 264 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 258 time to evaluate : 1.401 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1391 time to fit residues: 3.2950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 0.0060 chunk 122 optimal weight: 9.9990 chunk 131 optimal weight: 20.0000 chunk 78 optimal weight: 0.9990 chunk 57 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 130 optimal weight: 0.4980 chunk 86 optimal weight: 0.0270 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 ASN B 175 ASN ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 11596 Z= 0.123 Angle : 0.488 6.709 15881 Z= 0.238 Chirality : 0.044 0.147 1783 Planarity : 0.005 0.044 2112 Dihedral : 3.770 17.674 1546 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer Outliers : 0.48 % 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: -0.79 (0.21), residues: 1457 helix: -1.01 (0.55), residues: 79 sheet: 0.02 (0.26), residues: 386 loop : -0.71 (0.19), residues: 992 *********************** 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 287 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 281 time to evaluate : 1.350 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 283 average time/residue: 0.2321 time to fit residues: 93.6662 Evaluate side-chains 274 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 271 time to evaluate : 1.536 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1208 time to fit residues: 2.5977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 0.9980 chunk 84 optimal weight: 8.9990 chunk 65 optimal weight: 8.9990 chunk 96 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 133 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 92 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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** ** B 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 60 ASN C 342 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 11596 Z= 0.210 Angle : 0.516 6.682 15881 Z= 0.251 Chirality : 0.046 0.151 1783 Planarity : 0.005 0.042 2112 Dihedral : 3.902 18.357 1546 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer Outliers : 0.16 % 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: -0.75 (0.21), residues: 1457 helix: -0.94 (0.54), residues: 79 sheet: -0.02 (0.26), residues: 390 loop : -0.65 (0.20), residues: 988 ********************** 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 267 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 265 time to evaluate : 1.570 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 265 average time/residue: 0.2309 time to fit residues: 87.6207 Evaluate side-chains 260 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 259 time to evaluate : 1.331 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1457 time to fit residues: 2.0441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 106 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 32 optimal weight: 20.0000 chunk 116 optimal weight: 20.0000 chunk 48 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 356 GLN C 86 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.109027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.084974 restraints weight = 16343.769| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 2.55 r_work: 0.2658 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2519 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.078 11596 Z= 0.418 Angle : 0.609 9.630 15881 Z= 0.300 Chirality : 0.049 0.161 1783 Planarity : 0.005 0.041 2112 Dihedral : 4.408 19.188 1546 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.21), residues: 1457 helix: -1.30 (0.53), residues: 79 sheet: -0.22 (0.26), residues: 390 loop : -0.79 (0.19), residues: 988 =============================================================================== Job complete usr+sys time: 2526.92 seconds wall clock time: 46 minutes 34.34 seconds (2794.34 seconds total)