Starting phenix.real_space_refine on Sat Mar 16 13:20:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ta3_41127/03_2024/8ta3_41127.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ta3_41127/03_2024/8ta3_41127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ta3_41127/03_2024/8ta3_41127.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ta3_41127/03_2024/8ta3_41127.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ta3_41127/03_2024/8ta3_41127.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ta3_41127/03_2024/8ta3_41127.pdb" } resolution = 2.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.198 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 46 5.16 5 Cl 2 4.86 5 C 4825 2.51 5 N 1194 2.21 5 O 1225 1.98 5 H 7545 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 25": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 172": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 235": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 277": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 290": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 297": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 309": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 343": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 350": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 357": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 361": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 363": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 404": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 408": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 428": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 471": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 493": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 558": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 25": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 172": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 235": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 277": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 290": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 297": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 309": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 311": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 343": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 350": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 357": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 361": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 363": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 404": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 408": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 428": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 471": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 493": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 558": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14837 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 7406 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 22, 'TRANS': 447} Chain breaks: 5 Chain: "B" Number of atoms: 7429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 7429 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 22, 'TRANS': 449} Chain breaks: 5 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.36, per 1000 atoms: 0.43 Number of scatterers: 14837 At special positions: 0 Unit cell: (78.518, 75.68, 117.304, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 2 17.00 S 46 16.00 O 1225 8.00 N 1194 7.00 C 4825 6.00 H 7545 1.00 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: 12.07 Conformation dependent library (CDL) restraints added in 1.5 seconds 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1744 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 3 sheets defined 76.9% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 89 through 126 removed outlier: 3.520A pdb=" N ALA A 102 " --> pdb=" O GLY A 98 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN A 119 " --> pdb=" O CYS A 115 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 156 Proline residue: A 141 - end of helix Processing helix chain 'A' and resid 157 through 160 removed outlier: 3.661A pdb=" N VAL A 160 " --> pdb=" O PRO A 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 157 through 160' Processing helix chain 'A' and resid 163 through 172 Processing helix chain 'A' and resid 181 through 198 removed outlier: 3.558A pdb=" N SER A 198 " --> pdb=" O CYS A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 223 Processing helix chain 'A' and resid 234 through 253 removed outlier: 3.594A pdb=" N ALA A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 267 Processing helix chain 'A' and resid 272 through 296 removed outlier: 3.676A pdb=" N VAL A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 320 through 352 removed outlier: 3.506A pdb=" N VAL A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 362 removed outlier: 4.061A pdb=" N PHE A 358 " --> pdb=" O THR A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 379 Processing helix chain 'A' and resid 382 through 388 removed outlier: 3.967A pdb=" N GLN A 385 " --> pdb=" O GLY A 382 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA A 388 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 401 Processing helix chain 'A' and resid 421 through 425 Processing helix chain 'A' and resid 430 through 450 removed outlier: 3.773A pdb=" N TRP A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 481 Processing helix chain 'A' and resid 495 through 513 removed outlier: 3.920A pdb=" N TYR A 499 " --> pdb=" O VAL A 495 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A 508 " --> pdb=" O ALA A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 526 Processing helix chain 'A' and resid 530 through 547 removed outlier: 3.662A pdb=" N SER A 547 " --> pdb=" O ALA A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 560 Processing helix chain 'B' and resid 89 through 125 Processing helix chain 'B' and resid 129 through 156 removed outlier: 3.611A pdb=" N TYR B 140 " --> pdb=" O ALA B 136 " (cutoff:3.500A) Proline residue: B 141 - end of helix Processing helix chain 'B' and resid 157 through 160 Processing helix chain 'B' and resid 163 through 172 removed outlier: 3.509A pdb=" N ARG B 172 " --> pdb=" O LYS B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 198 Processing helix chain 'B' and resid 204 through 223 Processing helix chain 'B' and resid 232 through 253 removed outlier: 3.714A pdb=" N ALA B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 267 removed outlier: 3.511A pdb=" N VAL B 259 " --> pdb=" O PRO B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 293 Processing helix chain 'B' and resid 317 through 319 No H-bonds generated for 'chain 'B' and resid 317 through 319' Processing helix chain 'B' and resid 320 through 352 removed outlier: 3.581A pdb=" N PHE B 324 " --> pdb=" O GLU B 320 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 346 " --> pdb=" O ASN B 342 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET B 349 " --> pdb=" O ILE B 345 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN B 352 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 360 Processing helix chain 'B' and resid 364 through 379 Processing helix chain 'B' and resid 382 through 388 removed outlier: 4.141A pdb=" N GLN B 385 " --> pdb=" O GLY B 382 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA B 388 " --> pdb=" O GLN B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 401 Processing helix chain 'B' and resid 420 through 425 Processing helix chain 'B' and resid 430 through 450 removed outlier: 3.881A pdb=" N TRP B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 481 removed outlier: 3.548A pdb=" N ILE B 465 " --> pdb=" O PRO B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 513 removed outlier: 3.945A pdb=" N TYR B 499 " --> pdb=" O VAL B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 526 Processing helix chain 'B' and resid 530 through 547 removed outlier: 3.948A pdb=" N SER B 547 " --> pdb=" O ALA B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 560 Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 18 Processing sheet with id=AA2, first strand: chain 'A' and resid 269 through 271 removed outlier: 3.656A pdb=" N PHE A 270 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE B 270 " --> pdb=" O PHE A 270 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 16 through 18 528 hydrogen bonds defined for protein. 1542 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: 4.91 Time building geometry restraints manager: 12.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 7531 1.12 - 1.30: 1106 1.30 - 1.47: 2809 1.47 - 1.65: 3489 1.65 - 1.82: 78 Bond restraints: 15013 Sorted by residual: bond pdb=" N LEU A 318 " pdb=" H LEU A 318 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N THR A 169 " pdb=" H THR A 169 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N LEU B 318 " pdb=" H LEU B 318 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" NE ARG A 471 " pdb=" HE ARG A 471 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N LYS A 221 " pdb=" H LYS A 221 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 ... (remaining 15008 not shown) Histogram of bond angle deviations from ideal: 96.15 - 103.96: 130 103.96 - 111.78: 15878 111.78 - 119.60: 5974 119.60 - 127.41: 5102 127.41 - 135.23: 90 Bond angle restraints: 27174 Sorted by residual: angle pdb=" CA ASP B 402 " pdb=" CB ASP B 402 " pdb=" CG ASP B 402 " ideal model delta sigma weight residual 112.60 118.97 -6.37 1.00e+00 1.00e+00 4.06e+01 angle pdb=" N PRO B 426 " pdb=" CA PRO B 426 " pdb=" CB PRO B 426 " ideal model delta sigma weight residual 103.19 106.58 -3.39 5.60e-01 3.19e+00 3.65e+01 angle pdb=" CA PHE B 401 " pdb=" CB PHE B 401 " pdb=" CG PHE B 401 " ideal model delta sigma weight residual 113.80 119.64 -5.84 1.00e+00 1.00e+00 3.41e+01 angle pdb=" CA PHE A 401 " pdb=" CB PHE A 401 " pdb=" CG PHE A 401 " ideal model delta sigma weight residual 113.80 119.44 -5.64 1.00e+00 1.00e+00 3.18e+01 angle pdb=" CD ARG A 471 " pdb=" NE ARG A 471 " pdb=" CZ ARG A 471 " ideal model delta sigma weight residual 124.40 132.27 -7.87 1.40e+00 5.10e-01 3.16e+01 ... (remaining 27169 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.64: 6392 16.64 - 33.29: 345 33.29 - 49.93: 101 49.93 - 66.57: 208 66.57 - 83.22: 18 Dihedral angle restraints: 7064 sinusoidal: 3756 harmonic: 3308 Sorted by residual: dihedral pdb=" CA LEU B 176 " pdb=" C LEU B 176 " pdb=" N LYS B 177 " pdb=" CA LYS B 177 " ideal model delta harmonic sigma weight residual 180.00 -151.02 -28.98 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA LEU A 176 " pdb=" C LEU A 176 " pdb=" N LYS A 177 " pdb=" CA LYS A 177 " ideal model delta harmonic sigma weight residual -180.00 -152.68 -27.32 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA GLU B 231 " pdb=" C GLU B 231 " pdb=" N ASN B 232 " pdb=" CA ASN B 232 " ideal model delta harmonic sigma weight residual 180.00 153.62 26.38 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 7061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 788 0.078 - 0.155: 304 0.155 - 0.232: 87 0.232 - 0.310: 15 0.310 - 0.387: 4 Chirality restraints: 1198 Sorted by residual: chirality pdb=" CA PRO A 380 " pdb=" N PRO A 380 " pdb=" C PRO A 380 " pdb=" CB PRO A 380 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.39 2.00e-01 2.50e+01 3.74e+00 chirality pdb=" CA PRO B 380 " pdb=" N PRO B 380 " pdb=" C PRO B 380 " pdb=" CB PRO B 380 " both_signs ideal model delta sigma weight residual False 2.72 2.35 0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" CA THR A 420 " pdb=" N THR A 420 " pdb=" C THR A 420 " pdb=" CB THR A 420 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.37 2.00e-01 2.50e+01 3.40e+00 ... (remaining 1195 not shown) Planarity restraints: 2129 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 363 " 0.269 9.50e-02 1.11e+02 1.37e-01 2.51e+02 pdb=" NE ARG A 363 " 0.097 2.00e-02 2.50e+03 pdb=" CZ ARG A 363 " 0.068 2.00e-02 2.50e+03 pdb=" NH1 ARG A 363 " 0.043 2.00e-02 2.50e+03 pdb=" NH2 ARG A 363 " 0.045 2.00e-02 2.50e+03 pdb="HH11 ARG A 363 " -0.216 2.00e-02 2.50e+03 pdb="HH12 ARG A 363 " 0.102 2.00e-02 2.50e+03 pdb="HH21 ARG A 363 " -0.149 2.00e-02 2.50e+03 pdb="HH22 ARG A 363 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 106 " 0.144 2.00e-02 2.50e+03 5.38e-02 1.16e+02 pdb=" CG TRP A 106 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 TRP A 106 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP A 106 " -0.044 2.00e-02 2.50e+03 pdb=" NE1 TRP A 106 " -0.058 2.00e-02 2.50e+03 pdb=" CE2 TRP A 106 " -0.032 2.00e-02 2.50e+03 pdb=" CE3 TRP A 106 " -0.049 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 106 " 0.014 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 106 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP A 106 " 0.030 2.00e-02 2.50e+03 pdb=" HD1 TRP A 106 " 0.035 2.00e-02 2.50e+03 pdb=" HE1 TRP A 106 " -0.041 2.00e-02 2.50e+03 pdb=" HE3 TRP A 106 " -0.071 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 106 " 0.041 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 106 " -0.003 2.00e-02 2.50e+03 pdb=" HH2 TRP A 106 " 0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 179 " -0.129 2.00e-02 2.50e+03 6.01e-02 1.08e+02 pdb=" CG TYR B 179 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR B 179 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TYR B 179 " 0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR B 179 " 0.037 2.00e-02 2.50e+03 pdb=" CE2 TYR B 179 " 0.044 2.00e-02 2.50e+03 pdb=" CZ TYR B 179 " 0.017 2.00e-02 2.50e+03 pdb=" OH TYR B 179 " -0.135 2.00e-02 2.50e+03 pdb=" HD1 TYR B 179 " 0.018 2.00e-02 2.50e+03 pdb=" HD2 TYR B 179 " 0.014 2.00e-02 2.50e+03 pdb=" HE1 TYR B 179 " 0.016 2.00e-02 2.50e+03 pdb=" HE2 TYR B 179 " 0.016 2.00e-02 2.50e+03 ... (remaining 2126 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 564 2.17 - 2.78: 24825 2.78 - 3.39: 42225 3.39 - 3.99: 57740 3.99 - 4.60: 81254 Nonbonded interactions: 206608 Sorted by model distance: nonbonded pdb=" OE2 GLU B 264 " pdb=" HG SER B 516 " model vdw 1.565 1.850 nonbonded pdb=" OE2 GLU A 264 " pdb=" HG SER A 516 " model vdw 1.581 1.850 nonbonded pdb=" OE2 GLU B 395 " pdb=" HG SER B 419 " model vdw 1.628 1.850 nonbonded pdb=" OE1 GLU A 320 " pdb=" HH TYR A 499 " model vdw 1.632 1.850 nonbonded pdb=" HG SER B 392 " pdb=" OE1 GLU B 395 " model vdw 1.636 1.850 ... (remaining 206603 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' selection = (chain 'B' and (resid 14 through 487 or resid 491 through 566 or resid 901)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 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: 0.210 Extract box with map and model: 4.510 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 47.140 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.040 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:13.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 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 : 0.013 0.044 7468 Z= 0.845 Angle : 1.816 7.868 10153 Z= 1.266 Chirality : 0.091 0.387 1198 Planarity : 0.013 0.150 1243 Dihedral : 13.070 83.216 2599 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 0.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.51 % Favored : 97.39 % Rotamer: Outliers : 0.92 % Allowed : 2.09 % Favored : 96.99 % Cbeta Deviations : 0.11 % 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: -0.45 (0.24), residues: 918 helix: -0.07 (0.17), residues: 678 sheet: None (None), residues: 0 loop : -0.53 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.098 0.016 TRP A 106 HIS 0.017 0.006 HIS B 210 PHE 0.084 0.015 PHE B 93 TYR 0.127 0.015 TYR B 179 ARG 0.008 0.001 ARG A 343 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 118 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ARG cc_start: 0.7321 (mtm180) cc_final: 0.7110 (mtm180) REVERT: A 167 MET cc_start: 0.8493 (mmm) cc_final: 0.8207 (mmm) REVERT: A 178 GLU cc_start: 0.7299 (mt-10) cc_final: 0.7051 (mm-30) REVERT: A 404 ARG cc_start: 0.8549 (mmm160) cc_final: 0.7683 (mmm160) REVERT: A 422 GLN cc_start: 0.6820 (mm110) cc_final: 0.5753 (mp10) REVERT: A 441 MET cc_start: 0.8322 (mmp) cc_final: 0.8119 (mmm) REVERT: A 471 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.6091 (mmt-90) REVERT: A 535 MET cc_start: 0.8024 (mtp) cc_final: 0.7759 (mtp) REVERT: B 101 MET cc_start: 0.8164 (tpt) cc_final: 0.7602 (tpt) REVERT: B 117 GLN cc_start: 0.7180 (mt0) cc_final: 0.6920 (mp10) REVERT: B 273 ARG cc_start: 0.7390 (mtp-110) cc_final: 0.7000 (ttp-110) REVERT: B 344 LYS cc_start: 0.8351 (tptt) cc_final: 0.8133 (mmmm) REVERT: B 349 MET cc_start: 0.7592 (ppp) cc_final: 0.7211 (mtt) REVERT: B 363 ARG cc_start: 0.6483 (mmm160) cc_final: 0.5952 (tpp80) REVERT: B 369 LEU cc_start: 0.8395 (mt) cc_final: 0.8041 (mp) REVERT: B 383 PHE cc_start: 0.8692 (t80) cc_final: 0.8469 (t80) REVERT: B 404 ARG cc_start: 0.8192 (mtp85) cc_final: 0.7402 (mtm-85) REVERT: B 441 MET cc_start: 0.8226 (mmm) cc_final: 0.7972 (mmm) REVERT: B 445 MET cc_start: 0.8531 (mtt) cc_final: 0.7916 (mtt) REVERT: B 450 THR cc_start: 0.7915 (m) cc_final: 0.7404 (p) REVERT: B 477 MET cc_start: 0.7944 (mmm) cc_final: 0.7744 (mmm) REVERT: B 558 ARG cc_start: 0.8261 (mtp85) cc_final: 0.7830 (mtm110) outliers start: 7 outliers final: 2 residues processed: 124 average time/residue: 2.7272 time to fit residues: 356.0202 Evaluate side-chains 99 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 96 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 521 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 GLN B 422 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7468 Z= 0.239 Angle : 0.636 7.447 10153 Z= 0.355 Chirality : 0.039 0.131 1198 Planarity : 0.006 0.051 1243 Dihedral : 5.299 44.569 1005 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.44 % Allowed : 5.10 % Favored : 93.46 % 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: 1.41 (0.26), residues: 918 helix: 1.71 (0.19), residues: 685 sheet: -0.30 (1.19), residues: 18 loop : -1.50 (0.37), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 121 HIS 0.007 0.002 HIS A 513 PHE 0.020 0.002 PHE A 459 TYR 0.014 0.002 TYR A 275 ARG 0.004 0.001 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 ARG cc_start: 0.7296 (mtm180) cc_final: 0.6934 (mtm-85) REVERT: A 101 MET cc_start: 0.7704 (tpt) cc_final: 0.7028 (tpt) REVERT: A 167 MET cc_start: 0.8495 (mmm) cc_final: 0.8274 (mmm) REVERT: A 314 PHE cc_start: 0.7386 (m-80) cc_final: 0.7040 (m-80) REVERT: A 348 VAL cc_start: 0.8069 (OUTLIER) cc_final: 0.7835 (t) REVERT: A 404 ARG cc_start: 0.8371 (mmm160) cc_final: 0.7682 (mmm160) REVERT: A 535 MET cc_start: 0.7739 (mtp) cc_final: 0.7510 (mtp) REVERT: B 101 MET cc_start: 0.7905 (tpt) cc_final: 0.7673 (tpt) REVERT: B 117 GLN cc_start: 0.6989 (mt0) cc_final: 0.6706 (mp10) REVERT: B 166 GLU cc_start: 0.8490 (mp0) cc_final: 0.8205 (mp0) REVERT: B 167 MET cc_start: 0.8305 (mmm) cc_final: 0.8011 (mmp) REVERT: B 273 ARG cc_start: 0.7284 (mtp-110) cc_final: 0.6979 (ttt-90) REVERT: B 349 MET cc_start: 0.7554 (ppp) cc_final: 0.6875 (mmp) REVERT: B 450 THR cc_start: 0.7560 (m) cc_final: 0.7102 (p) REVERT: B 477 MET cc_start: 0.7767 (mmm) cc_final: 0.7504 (mmm) REVERT: B 486 HIS cc_start: 0.5064 (OUTLIER) cc_final: 0.4018 (p90) REVERT: B 558 ARG cc_start: 0.7894 (mtp85) cc_final: 0.7310 (mtm180) outliers start: 11 outliers final: 3 residues processed: 110 average time/residue: 2.4070 time to fit residues: 281.7584 Evaluate side-chains 101 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 486 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7468 Z= 0.256 Angle : 0.601 7.378 10153 Z= 0.331 Chirality : 0.040 0.140 1198 Planarity : 0.005 0.052 1243 Dihedral : 4.744 36.092 1001 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.44 % Allowed : 6.94 % Favored : 91.62 % 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: 1.63 (0.27), residues: 918 helix: 1.94 (0.19), residues: 683 sheet: -0.30 (1.18), residues: 18 loop : -1.68 (0.38), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 444 HIS 0.006 0.002 HIS A 513 PHE 0.022 0.002 PHE B 463 TYR 0.012 0.002 TYR A 275 ARG 0.006 0.001 ARG A 471 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 103 time to evaluate : 0.969 Fit side-chains revert: symmetry clash REVERT: A 25 ARG cc_start: 0.7384 (mtm180) cc_final: 0.7061 (mtm-85) REVERT: A 101 MET cc_start: 0.7425 (tpt) cc_final: 0.6974 (tpt) REVERT: A 167 MET cc_start: 0.8427 (mmm) cc_final: 0.8202 (mmm) REVERT: A 172 ARG cc_start: 0.7785 (mtm-85) cc_final: 0.7505 (mtm-85) REVERT: A 314 PHE cc_start: 0.7439 (m-80) cc_final: 0.7069 (m-80) REVERT: A 349 MET cc_start: 0.7464 (OUTLIER) cc_final: 0.6654 (mpt) REVERT: A 351 LYS cc_start: 0.7713 (OUTLIER) cc_final: 0.7460 (mttp) REVERT: A 404 ARG cc_start: 0.8364 (mmm160) cc_final: 0.7591 (mmm160) REVERT: B 117 GLN cc_start: 0.6906 (mt0) cc_final: 0.6629 (mp10) REVERT: B 166 GLU cc_start: 0.8469 (mp0) cc_final: 0.8103 (mp0) REVERT: B 167 MET cc_start: 0.8258 (mmm) cc_final: 0.7967 (mmp) REVERT: B 349 MET cc_start: 0.7499 (ppp) cc_final: 0.6984 (mmp) REVERT: B 363 ARG cc_start: 0.6586 (mmm160) cc_final: 0.5913 (tpp80) REVERT: B 404 ARG cc_start: 0.8264 (mtp85) cc_final: 0.7551 (mtp-110) REVERT: B 450 THR cc_start: 0.7659 (m) cc_final: 0.7223 (p) REVERT: B 477 MET cc_start: 0.7741 (mmm) cc_final: 0.7474 (mmm) REVERT: B 486 HIS cc_start: 0.5102 (OUTLIER) cc_final: 0.4157 (p90) REVERT: B 558 ARG cc_start: 0.7905 (mtp85) cc_final: 0.7464 (mtp180) outliers start: 11 outliers final: 4 residues processed: 107 average time/residue: 2.6164 time to fit residues: 295.6269 Evaluate side-chains 105 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 98 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 486 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 2.9990 chunk 64 optimal weight: 0.3980 chunk 44 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7468 Z= 0.167 Angle : 0.511 6.465 10153 Z= 0.278 Chirality : 0.036 0.124 1198 Planarity : 0.005 0.051 1243 Dihedral : 4.493 35.826 1001 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.18 % Allowed : 7.72 % Favored : 91.10 % 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: 2.11 (0.28), residues: 918 helix: 2.34 (0.19), residues: 683 sheet: -0.14 (1.27), residues: 18 loop : -1.67 (0.38), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 444 HIS 0.002 0.001 HIS A 513 PHE 0.014 0.001 PHE B 463 TYR 0.008 0.001 TYR A 275 ARG 0.002 0.000 ARG A 363 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 98 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 MET cc_start: 0.7341 (tpt) cc_final: 0.6933 (tpt) REVERT: A 167 MET cc_start: 0.8430 (mmm) cc_final: 0.8224 (mmm) REVERT: A 314 PHE cc_start: 0.7396 (m-80) cc_final: 0.7063 (m-80) REVERT: A 348 VAL cc_start: 0.8148 (OUTLIER) cc_final: 0.7944 (t) REVERT: A 349 MET cc_start: 0.7447 (OUTLIER) cc_final: 0.6531 (mpt) REVERT: A 351 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.7388 (mttp) REVERT: A 404 ARG cc_start: 0.8295 (mmm160) cc_final: 0.7562 (mmm160) REVERT: B 117 GLN cc_start: 0.6823 (mt0) cc_final: 0.6526 (mp10) REVERT: B 166 GLU cc_start: 0.8461 (mp0) cc_final: 0.7821 (mp0) REVERT: B 167 MET cc_start: 0.8246 (mmm) cc_final: 0.7934 (mmp) REVERT: B 238 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7310 (tt0) REVERT: B 395 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7116 (mt-10) REVERT: B 404 ARG cc_start: 0.8176 (mtp85) cc_final: 0.7484 (mtp-110) REVERT: B 450 THR cc_start: 0.7620 (m) cc_final: 0.7156 (p) REVERT: B 477 MET cc_start: 0.7703 (mmm) cc_final: 0.7486 (mmm) REVERT: B 486 HIS cc_start: 0.5100 (OUTLIER) cc_final: 0.4069 (p90) REVERT: B 558 ARG cc_start: 0.7888 (mtp85) cc_final: 0.7434 (mtp180) outliers start: 9 outliers final: 3 residues processed: 101 average time/residue: 2.5584 time to fit residues: 273.6753 Evaluate side-chains 105 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 97 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 486 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 0 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7468 Z= 0.289 Angle : 0.576 6.902 10153 Z= 0.316 Chirality : 0.040 0.141 1198 Planarity : 0.005 0.051 1243 Dihedral : 4.595 34.474 1001 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.57 % Allowed : 7.46 % Favored : 90.97 % 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: 1.83 (0.27), residues: 918 helix: 2.13 (0.19), residues: 683 sheet: -0.06 (1.24), residues: 18 loop : -1.76 (0.38), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 444 HIS 0.002 0.001 HIS B 513 PHE 0.020 0.002 PHE B 463 TYR 0.012 0.002 TYR A 275 ARG 0.005 0.000 ARG A 471 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 100 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7397 (tt0) cc_final: 0.6728 (tm-30) REVERT: A 167 MET cc_start: 0.8426 (mmm) cc_final: 0.8184 (mmm) REVERT: A 349 MET cc_start: 0.7430 (OUTLIER) cc_final: 0.6521 (mpt) REVERT: A 351 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7479 (mttp) REVERT: A 369 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7835 (mp) REVERT: A 404 ARG cc_start: 0.8358 (mmm160) cc_final: 0.7597 (mmm160) REVERT: B 117 GLN cc_start: 0.6851 (mt0) cc_final: 0.6570 (mp10) REVERT: B 166 GLU cc_start: 0.8470 (mp0) cc_final: 0.7822 (mp0) REVERT: B 167 MET cc_start: 0.8263 (mmm) cc_final: 0.7956 (mmp) REVERT: B 238 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7312 (tt0) REVERT: B 404 ARG cc_start: 0.8251 (mtp85) cc_final: 0.7549 (mtp-110) REVERT: B 450 THR cc_start: 0.7700 (m) cc_final: 0.7257 (p) REVERT: B 477 MET cc_start: 0.7705 (mmm) cc_final: 0.7498 (mmm) REVERT: B 486 HIS cc_start: 0.5103 (OUTLIER) cc_final: 0.4138 (p90) REVERT: B 558 ARG cc_start: 0.7898 (mtp85) cc_final: 0.7448 (mtp180) outliers start: 12 outliers final: 4 residues processed: 105 average time/residue: 2.7777 time to fit residues: 307.5779 Evaluate side-chains 107 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 98 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 486 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7468 Z= 0.255 Angle : 0.556 7.609 10153 Z= 0.303 Chirality : 0.039 0.136 1198 Planarity : 0.005 0.052 1243 Dihedral : 4.551 34.009 1001 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.70 % Allowed : 7.98 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.27), residues: 918 helix: 2.22 (0.19), residues: 682 sheet: 0.05 (1.25), residues: 18 loop : -1.79 (0.38), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 444 HIS 0.002 0.001 HIS A 210 PHE 0.018 0.002 PHE B 463 TYR 0.010 0.001 TYR A 275 ARG 0.003 0.000 ARG A 471 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7418 (tt0) cc_final: 0.6737 (tm-30) REVERT: A 167 MET cc_start: 0.8387 (mmm) cc_final: 0.8149 (mmm) REVERT: A 273 ARG cc_start: 0.7995 (mtp85) cc_final: 0.7402 (mtm110) REVERT: A 349 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.6500 (mpt) REVERT: A 351 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.7390 (mttp) REVERT: A 369 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7812 (mp) REVERT: A 404 ARG cc_start: 0.8367 (mmm160) cc_final: 0.7599 (mmm160) REVERT: B 117 GLN cc_start: 0.6870 (mt0) cc_final: 0.6581 (mp10) REVERT: B 166 GLU cc_start: 0.8454 (mp0) cc_final: 0.7781 (mp0) REVERT: B 167 MET cc_start: 0.8259 (mmm) cc_final: 0.7967 (mmp) REVERT: B 238 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7222 (tt0) REVERT: B 363 ARG cc_start: 0.6859 (mmm160) cc_final: 0.5949 (tpp80) REVERT: B 404 ARG cc_start: 0.8235 (mtp85) cc_final: 0.7540 (mtp-110) REVERT: B 450 THR cc_start: 0.7851 (m) cc_final: 0.7356 (p) REVERT: B 477 MET cc_start: 0.7724 (mmm) cc_final: 0.7511 (mmm) REVERT: B 486 HIS cc_start: 0.5105 (OUTLIER) cc_final: 0.4125 (p90) REVERT: B 558 ARG cc_start: 0.7937 (mtp85) cc_final: 0.7491 (mtp180) outliers start: 13 outliers final: 4 residues processed: 106 average time/residue: 2.8569 time to fit residues: 318.8108 Evaluate side-chains 109 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 486 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7468 Z= 0.215 Angle : 0.528 7.540 10153 Z= 0.286 Chirality : 0.037 0.130 1198 Planarity : 0.005 0.051 1243 Dihedral : 4.436 33.573 1001 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.57 % Allowed : 8.90 % Favored : 89.53 % 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: 2.13 (0.28), residues: 918 helix: 2.40 (0.19), residues: 682 sheet: -0.06 (1.22), residues: 18 loop : -1.83 (0.37), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 121 HIS 0.002 0.001 HIS B 210 PHE 0.017 0.001 PHE B 463 TYR 0.009 0.001 TYR A 275 ARG 0.002 0.000 ARG A 471 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 101 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7419 (tt0) cc_final: 0.6736 (tm-30) REVERT: A 167 MET cc_start: 0.8390 (mmm) cc_final: 0.8168 (mmm) REVERT: A 349 MET cc_start: 0.7342 (OUTLIER) cc_final: 0.6415 (mpt) REVERT: A 351 LYS cc_start: 0.7678 (OUTLIER) cc_final: 0.7347 (mttp) REVERT: A 369 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7813 (mp) REVERT: A 404 ARG cc_start: 0.8357 (mmm160) cc_final: 0.7592 (mmm160) REVERT: B 22 MET cc_start: 0.6544 (mtp) cc_final: 0.5678 (mtt) REVERT: B 117 GLN cc_start: 0.6800 (mt0) cc_final: 0.6571 (mp10) REVERT: B 166 GLU cc_start: 0.8438 (mp0) cc_final: 0.7759 (mp0) REVERT: B 167 MET cc_start: 0.8248 (mmm) cc_final: 0.7961 (mmp) REVERT: B 238 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7100 (tt0) REVERT: B 404 ARG cc_start: 0.8192 (mtp85) cc_final: 0.7504 (mtp-110) REVERT: B 450 THR cc_start: 0.7832 (m) cc_final: 0.7321 (p) REVERT: B 477 MET cc_start: 0.7692 (mmm) cc_final: 0.7466 (mmm) REVERT: B 486 HIS cc_start: 0.5066 (OUTLIER) cc_final: 0.4207 (p90) REVERT: B 558 ARG cc_start: 0.7935 (mtp85) cc_final: 0.7489 (mtp180) outliers start: 12 outliers final: 3 residues processed: 106 average time/residue: 2.7066 time to fit residues: 304.4637 Evaluate side-chains 107 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 99 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 486 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 0.3980 chunk 57 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7468 Z= 0.211 Angle : 0.526 9.029 10153 Z= 0.283 Chirality : 0.037 0.132 1198 Planarity : 0.005 0.052 1243 Dihedral : 4.396 33.260 1001 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.44 % Allowed : 9.42 % Favored : 89.14 % 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: 2.18 (0.28), residues: 918 helix: 2.45 (0.19), residues: 682 sheet: -0.18 (1.21), residues: 18 loop : -1.83 (0.38), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 121 HIS 0.002 0.001 HIS B 210 PHE 0.017 0.001 PHE B 463 TYR 0.009 0.001 TYR A 275 ARG 0.005 0.000 ARG B 277 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 103 time to evaluate : 1.130 Fit side-chains revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7416 (tt0) cc_final: 0.6744 (tm-30) REVERT: A 167 MET cc_start: 0.8381 (mmm) cc_final: 0.8166 (mmm) REVERT: A 349 MET cc_start: 0.7325 (OUTLIER) cc_final: 0.6407 (mpt) REVERT: A 351 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7341 (mttp) REVERT: A 369 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7835 (mp) REVERT: A 404 ARG cc_start: 0.8360 (mmm160) cc_final: 0.7586 (mmm160) REVERT: B 117 GLN cc_start: 0.6779 (mt0) cc_final: 0.6564 (mp10) REVERT: B 166 GLU cc_start: 0.8407 (mp0) cc_final: 0.8139 (mp0) REVERT: B 167 MET cc_start: 0.8248 (mmm) cc_final: 0.7954 (mmp) REVERT: B 363 ARG cc_start: 0.6863 (mmm160) cc_final: 0.5920 (tpp80) REVERT: B 404 ARG cc_start: 0.8206 (mtp85) cc_final: 0.7487 (mtp-110) REVERT: B 450 THR cc_start: 0.7787 (m) cc_final: 0.7263 (p) REVERT: B 477 MET cc_start: 0.7684 (mmm) cc_final: 0.7456 (mmm) REVERT: B 486 HIS cc_start: 0.5053 (OUTLIER) cc_final: 0.4254 (p90) REVERT: B 558 ARG cc_start: 0.7970 (mtp85) cc_final: 0.7519 (mtp180) outliers start: 11 outliers final: 3 residues processed: 107 average time/residue: 2.6360 time to fit residues: 298.0506 Evaluate side-chains 111 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 104 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 486 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN B 422 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7468 Z= 0.209 Angle : 0.521 6.990 10153 Z= 0.281 Chirality : 0.037 0.130 1198 Planarity : 0.005 0.052 1243 Dihedral : 4.351 33.133 1001 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.05 % Allowed : 10.08 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.28), residues: 918 helix: 2.50 (0.19), residues: 682 sheet: -0.33 (1.18), residues: 18 loop : -1.84 (0.38), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 121 HIS 0.002 0.001 HIS B 210 PHE 0.016 0.001 PHE B 463 TYR 0.009 0.001 TYR A 275 ARG 0.003 0.000 ARG B 277 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 105 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7393 (tt0) cc_final: 0.6731 (tm-30) REVERT: A 167 MET cc_start: 0.8375 (mmm) cc_final: 0.8161 (mmm) REVERT: A 349 MET cc_start: 0.7318 (OUTLIER) cc_final: 0.6396 (mpt) REVERT: A 351 LYS cc_start: 0.7676 (OUTLIER) cc_final: 0.7352 (mttp) REVERT: A 404 ARG cc_start: 0.8365 (mmm160) cc_final: 0.7589 (mmm160) REVERT: B 166 GLU cc_start: 0.8403 (mp0) cc_final: 0.8137 (mp0) REVERT: B 167 MET cc_start: 0.8253 (mmm) cc_final: 0.7959 (mmp) REVERT: B 363 ARG cc_start: 0.6881 (mmm160) cc_final: 0.5927 (tpp80) REVERT: B 404 ARG cc_start: 0.8217 (mtp85) cc_final: 0.7496 (mtp-110) REVERT: B 450 THR cc_start: 0.7796 (m) cc_final: 0.7270 (p) REVERT: B 477 MET cc_start: 0.7681 (mmm) cc_final: 0.7455 (mmm) REVERT: B 486 HIS cc_start: 0.5042 (OUTLIER) cc_final: 0.4235 (p90) REVERT: B 558 ARG cc_start: 0.7987 (mtp85) cc_final: 0.7527 (mtp180) outliers start: 8 outliers final: 3 residues processed: 109 average time/residue: 2.6217 time to fit residues: 302.3882 Evaluate side-chains 109 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 103 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 486 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 79 optimal weight: 0.0470 chunk 22 optimal weight: 2.9990 overall best weight: 1.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7468 Z= 0.203 Angle : 0.531 10.646 10153 Z= 0.282 Chirality : 0.037 0.128 1198 Planarity : 0.005 0.052 1243 Dihedral : 4.334 33.039 1001 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.05 % Allowed : 10.21 % Favored : 88.74 % 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: 2.29 (0.28), residues: 918 helix: 2.54 (0.19), residues: 682 sheet: -0.42 (1.18), residues: 18 loop : -1.85 (0.37), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 121 HIS 0.002 0.001 HIS B 210 PHE 0.016 0.001 PHE B 463 TYR 0.009 0.001 TYR A 275 ARG 0.002 0.000 ARG A 309 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 105 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7389 (tt0) cc_final: 0.6728 (tm-30) REVERT: A 167 MET cc_start: 0.8372 (mmm) cc_final: 0.8043 (mmm) REVERT: A 351 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.7345 (mttp) REVERT: A 404 ARG cc_start: 0.8351 (mmm160) cc_final: 0.7576 (mmm160) REVERT: B 166 GLU cc_start: 0.8401 (mp0) cc_final: 0.8135 (mp0) REVERT: B 167 MET cc_start: 0.8249 (mmm) cc_final: 0.7959 (mmp) REVERT: B 363 ARG cc_start: 0.6889 (mmm160) cc_final: 0.5941 (tpp80) REVERT: B 404 ARG cc_start: 0.8214 (mtp85) cc_final: 0.7493 (mtp-110) REVERT: B 450 THR cc_start: 0.7788 (m) cc_final: 0.7263 (p) REVERT: B 477 MET cc_start: 0.7675 (mmm) cc_final: 0.7449 (mmm) REVERT: B 486 HIS cc_start: 0.5034 (OUTLIER) cc_final: 0.4304 (p90) REVERT: B 558 ARG cc_start: 0.7989 (mtp85) cc_final: 0.7525 (mtp180) outliers start: 8 outliers final: 3 residues processed: 109 average time/residue: 2.6081 time to fit residues: 301.0962 Evaluate side-chains 107 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 102 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 486 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.145562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.110840 restraints weight = 20563.574| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.60 r_work: 0.3025 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7468 Z= 0.164 Angle : 0.503 10.409 10153 Z= 0.266 Chirality : 0.036 0.121 1198 Planarity : 0.005 0.052 1243 Dihedral : 4.217 32.857 1001 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.92 % Allowed : 10.34 % Favored : 88.74 % 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: 2.51 (0.28), residues: 918 helix: 2.71 (0.19), residues: 682 sheet: -0.47 (1.17), residues: 18 loop : -1.76 (0.38), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 121 HIS 0.002 0.001 HIS B 210 PHE 0.014 0.001 PHE B 463 TYR 0.008 0.001 TYR B 140 ARG 0.002 0.000 ARG A 311 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5880.33 seconds wall clock time: 102 minutes 56.26 seconds (6176.26 seconds total)