Starting phenix.real_space_refine on Fri Jul 19 14:34:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xou_33359/07_2024/7xou_33359.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xou_33359/07_2024/7xou_33359.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/7xou_33359/07_2024/7xou_33359.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xou_33359/07_2024/7xou_33359.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xou_33359/07_2024/7xou_33359.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xou_33359/07_2024/7xou_33359.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 5231 2.51 5 N 1433 2.21 5 O 1520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 38": "NH1" <-> "NH2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "R ARG 73": "NH1" <-> "NH2" Residue "R ARG 310": "NH1" <-> "NH2" Residue "R ARG 345": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 8247 Number of models: 1 Model: "" Number of chains: 7 Chain: "L" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 77 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1884 Classifications: {'peptide': 227} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 2288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2288 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 11, 'TRANS': 275} Chain breaks: 1 Time building chain proxies: 5.01, per 1000 atoms: 0.61 Number of scatterers: 8247 At special positions: 0 Unit cell: (90.246, 91.26, 129.792, 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 63 16.00 O 1520 8.00 N 1433 7.00 C 5231 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 114 " - pdb=" SG CYS R 196 " distance=2.04 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.22 Conformation dependent library (CDL) restraints added in 1.7 seconds 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1968 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 11 sheets defined 39.8% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 12 through 38 removed outlier: 3.545A pdb=" N ILE A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 removed outlier: 3.729A pdb=" N GLN A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 240 removed outlier: 3.860A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 236 through 240' Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 302 removed outlier: 3.584A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.917A pdb=" N TYR A 318 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.724A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 388 removed outlier: 3.626A pdb=" N ASP A 378 " --> pdb=" O ARG A 374 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N MET A 386 " --> pdb=" O ILE A 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 8 through 22 removed outlier: 3.670A pdb=" N ALA G 12 " --> pdb=" O SER G 8 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.575A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.824A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.800A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 69 removed outlier: 3.976A pdb=" N PHE R 52 " --> pdb=" O TYR R 48 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER R 55 " --> pdb=" O ILE R 51 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N GLY R 58 " --> pdb=" O LEU R 54 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN R 69 " --> pdb=" O VAL R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 94 removed outlier: 3.980A pdb=" N PHE R 79 " --> pdb=" O VAL R 75 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N LEU R 80 " --> pdb=" O THR R 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 95 through 105 Proline residue: R 101 - end of helix Processing helix chain 'R' and resid 110 through 144 removed outlier: 4.612A pdb=" N THR R 116 " --> pdb=" O ALA R 112 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR R 117 " --> pdb=" O VAL R 113 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL R 125 " --> pdb=" O MET R 121 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY R 141 " --> pdb=" O LEU R 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 154 through 173 Processing helix chain 'R' and resid 202 through 218 Processing helix chain 'R' and resid 219 through 244 removed outlier: 4.003A pdb=" N GLU R 243 " --> pdb=" O GLY R 239 " (cutoff:3.500A) Processing helix chain 'R' and resid 302 through 339 Proline residue: R 328 - end of helix Processing helix chain 'R' and resid 350 through 370 removed outlier: 4.044A pdb=" N SER R 359 " --> pdb=" O ILE R 355 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR R 361 " --> pdb=" O LEU R 357 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N SER R 362 " --> pdb=" O LEU R 358 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N SER R 363 " --> pdb=" O SER R 359 " (cutoff:3.500A) Proline residue: R 367 - end of helix Processing helix chain 'R' and resid 375 through 385 removed outlier: 4.054A pdb=" N LEU R 379 " --> pdb=" O LYS R 375 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA R 383 " --> pdb=" O LEU R 379 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.568A pdb=" N LEU A 45 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 9.657A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.687A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 61 removed outlier: 6.861A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.107A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.388A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.923A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.506A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.203A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.778A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP N 50 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 179 through 182 removed outlier: 3.606A pdb=" N ARG R 197 " --> pdb=" O SER R 180 " (cutoff:3.500A) 394 hydrogen bonds defined for protein. 1128 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: 2.15 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2680 1.34 - 1.46: 1989 1.46 - 1.58: 3647 1.58 - 1.70: 1 1.70 - 1.82: 92 Bond restraints: 8409 Sorted by residual: bond pdb=" O1 TYS L 2 " pdb=" S TYS L 2 " ideal model delta sigma weight residual 1.462 1.630 -0.168 2.00e-02 2.50e+03 7.07e+01 bond pdb=" OH TYS L 2 " pdb=" S TYS L 2 " ideal model delta sigma weight residual 1.679 1.531 0.148 2.00e-02 2.50e+03 5.48e+01 bond pdb=" N TRP L 5 " pdb=" CA TRP L 5 " ideal model delta sigma weight residual 1.458 1.432 0.027 1.08e-02 8.57e+03 6.04e+00 bond pdb=" C VAL R 183 " pdb=" N PRO R 184 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.19e+00 bond pdb=" C GLY L 4 " pdb=" N TRP L 5 " ideal model delta sigma weight residual 1.336 1.313 0.023 1.55e-02 4.16e+03 2.30e+00 ... (remaining 8404 not shown) Histogram of bond angle deviations from ideal: 99.74 - 106.59: 194 106.59 - 113.45: 4557 113.45 - 120.30: 3178 120.30 - 127.16: 3367 127.16 - 134.01: 83 Bond angle restraints: 11379 Sorted by residual: angle pdb=" N TRP L 5 " pdb=" CA TRP L 5 " pdb=" C TRP L 5 " ideal model delta sigma weight residual 112.30 105.02 7.28 1.36e+00 5.41e-01 2.87e+01 angle pdb=" C MET L 6 " pdb=" CA MET L 6 " pdb=" CB MET L 6 " ideal model delta sigma weight residual 116.54 110.40 6.14 1.15e+00 7.56e-01 2.85e+01 angle pdb=" CA MET L 6 " pdb=" C MET L 6 " pdb=" N ASP L 7 " ideal model delta sigma weight residual 119.52 115.50 4.02 7.90e-01 1.60e+00 2.58e+01 angle pdb=" N SER R 180 " pdb=" CA SER R 180 " pdb=" C SER R 180 " ideal model delta sigma weight residual 108.45 114.06 -5.61 1.26e+00 6.30e-01 1.98e+01 angle pdb=" N VAL R 183 " pdb=" CA VAL R 183 " pdb=" C VAL R 183 " ideal model delta sigma weight residual 108.88 116.53 -7.65 2.16e+00 2.14e-01 1.25e+01 ... (remaining 11374 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.06: 4464 16.06 - 32.12: 461 32.12 - 48.18: 83 48.18 - 64.24: 17 64.24 - 80.31: 7 Dihedral angle restraints: 5032 sinusoidal: 1998 harmonic: 3034 Sorted by residual: dihedral pdb=" CB CYS R 114 " pdb=" SG CYS R 114 " pdb=" SG CYS R 196 " pdb=" CB CYS R 196 " ideal model delta sinusoidal sigma weight residual 93.00 173.31 -80.31 1 1.00e+01 1.00e-02 7.98e+01 dihedral pdb=" CA LEU R 200 " pdb=" C LEU R 200 " pdb=" N PRO R 201 " pdb=" CA PRO R 201 " ideal model delta harmonic sigma weight residual 180.00 -147.78 -32.22 0 5.00e+00 4.00e-02 4.15e+01 dihedral pdb=" CA CYS R 94 " pdb=" C CYS R 94 " pdb=" N MET R 95 " pdb=" CA MET R 95 " ideal model delta harmonic sigma weight residual 180.00 -151.11 -28.89 0 5.00e+00 4.00e-02 3.34e+01 ... (remaining 5029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 795 0.035 - 0.069: 333 0.069 - 0.104: 118 0.104 - 0.139: 37 0.139 - 0.174: 4 Chirality restraints: 1287 Sorted by residual: chirality pdb=" CA THR R 350 " pdb=" N THR R 350 " pdb=" C THR R 350 " pdb=" CB THR R 350 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.53e-01 chirality pdb=" CA PRO R 201 " pdb=" N PRO R 201 " pdb=" C PRO R 201 " pdb=" CB PRO R 201 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.24e-01 chirality pdb=" CA THR R 174 " pdb=" N THR R 174 " pdb=" C THR R 174 " pdb=" CB THR R 174 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 7.01e-01 ... (remaining 1284 not shown) Planarity restraints: 1445 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET R 95 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.06e+00 pdb=" C MET R 95 " -0.035 2.00e-02 2.50e+03 pdb=" O MET R 95 " 0.013 2.00e-02 2.50e+03 pdb=" N PRO R 96 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET L 3 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.90e+00 pdb=" C MET L 3 " 0.034 2.00e-02 2.50e+03 pdb=" O MET L 3 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY L 4 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 242 " 0.010 2.00e-02 2.50e+03 1.44e-02 3.63e+00 pdb=" CG PHE R 242 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE R 242 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE R 242 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE R 242 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE R 242 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE R 242 " -0.001 2.00e-02 2.50e+03 ... (remaining 1442 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 783 2.74 - 3.28: 8415 3.28 - 3.82: 13572 3.82 - 4.36: 16321 4.36 - 4.90: 28075 Nonbonded interactions: 67166 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.205 2.440 nonbonded pdb=" OD2 ASP B 247 " pdb=" NH2 ARG B 251 " model vdw 2.206 2.520 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.209 2.440 nonbonded pdb=" OE2 GLU A 230 " pdb=" NH1 ARG A 232 " model vdw 2.209 2.520 nonbonded pdb=" O ASP A 368 " pdb=" ND2 ASN A 371 " model vdw 2.221 2.520 ... (remaining 67161 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.340 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: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.720 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6435 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.168 8409 Z= 0.227 Angle : 0.707 9.794 11379 Z= 0.395 Chirality : 0.045 0.174 1287 Planarity : 0.005 0.047 1445 Dihedral : 13.469 76.468 3055 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.11 % Allowed : 3.45 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -3.52 (0.22), residues: 1021 helix: -1.72 (0.22), residues: 384 sheet: -2.12 (0.30), residues: 221 loop : -2.94 (0.25), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 234 HIS 0.003 0.001 HIS A 357 PHE 0.033 0.002 PHE R 242 TYR 0.014 0.001 TYR B 59 ARG 0.005 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 192 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 291 LEU cc_start: 0.8099 (mp) cc_final: 0.7885 (mp) REVERT: B 155 ASN cc_start: 0.8405 (t0) cc_final: 0.7831 (t0) REVERT: N 72 ARG cc_start: 0.6911 (ptm160) cc_final: 0.5861 (ptp-170) REVERT: R 105 LYS cc_start: 0.4547 (mttm) cc_final: 0.4273 (mptt) REVERT: R 306 MET cc_start: 0.6633 (tpp) cc_final: 0.6323 (tpp) REVERT: R 309 LYS cc_start: 0.6598 (ttpp) cc_final: 0.6389 (ptmt) outliers start: 1 outliers final: 0 residues processed: 192 average time/residue: 0.2489 time to fit residues: 62.0287 Evaluate side-chains 152 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 42 optimal weight: 0.4980 chunk 26 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 79 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 HIS A 390 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN R 102 ASN R 181 ASN R 194 ASN R 238 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6460 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8409 Z= 0.165 Angle : 0.581 8.256 11379 Z= 0.303 Chirality : 0.042 0.157 1287 Planarity : 0.004 0.047 1445 Dihedral : 5.018 40.380 1133 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.56 % Allowed : 12.46 % Favored : 85.98 % 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: -1.77 (0.25), residues: 1021 helix: 0.12 (0.26), residues: 391 sheet: -1.30 (0.33), residues: 232 loop : -2.36 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 5 HIS 0.004 0.001 HIS A 387 PHE 0.017 0.001 PHE R 242 TYR 0.024 0.001 TYR N 60 ARG 0.001 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 165 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 291 LEU cc_start: 0.8008 (mp) cc_final: 0.7720 (mp) REVERT: G 48 ASP cc_start: 0.7817 (t70) cc_final: 0.7361 (p0) REVERT: N 72 ARG cc_start: 0.6947 (ptm160) cc_final: 0.5947 (ptp-170) REVERT: R 105 LYS cc_start: 0.4473 (mttm) cc_final: 0.4130 (mptt) REVERT: R 326 TRP cc_start: 0.7256 (m100) cc_final: 0.7024 (m100) outliers start: 14 outliers final: 8 residues processed: 170 average time/residue: 0.2283 time to fit residues: 51.5704 Evaluate side-chains 158 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 150 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain R residue 150 ARG Chi-restraints excluded: chain R residue 153 GLN Chi-restraints excluded: chain R residue 340 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6483 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8409 Z= 0.174 Angle : 0.578 7.558 11379 Z= 0.302 Chirality : 0.042 0.158 1287 Planarity : 0.004 0.045 1445 Dihedral : 4.888 39.764 1133 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.11 % Allowed : 15.24 % Favored : 82.65 % 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: -1.24 (0.26), residues: 1021 helix: 0.62 (0.27), residues: 388 sheet: -1.05 (0.33), residues: 233 loop : -2.11 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 5 HIS 0.003 0.001 HIS B 183 PHE 0.014 0.001 PHE R 107 TYR 0.017 0.001 TYR N 60 ARG 0.004 0.000 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 157 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: A 291 LEU cc_start: 0.7883 (mp) cc_final: 0.7626 (mp) REVERT: B 86 THR cc_start: 0.8628 (OUTLIER) cc_final: 0.8205 (p) REVERT: G 48 ASP cc_start: 0.7844 (t70) cc_final: 0.7435 (p0) REVERT: N 5 GLN cc_start: 0.7058 (OUTLIER) cc_final: 0.6759 (mp10) REVERT: N 72 ARG cc_start: 0.6962 (ptm160) cc_final: 0.5980 (ptp-170) REVERT: R 105 LYS cc_start: 0.4605 (mttm) cc_final: 0.4259 (mptt) outliers start: 19 outliers final: 10 residues processed: 164 average time/residue: 0.2484 time to fit residues: 54.5042 Evaluate side-chains 161 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 149 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain R residue 150 ARG Chi-restraints excluded: chain R residue 153 GLN Chi-restraints excluded: chain R residue 340 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 10 optimal weight: 0.0570 chunk 43 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 overall best weight: 2.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6603 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8409 Z= 0.303 Angle : 0.671 7.578 11379 Z= 0.350 Chirality : 0.046 0.150 1287 Planarity : 0.005 0.045 1445 Dihedral : 5.378 45.116 1133 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.67 % Allowed : 17.02 % Favored : 79.31 % 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: -1.48 (0.26), residues: 1021 helix: 0.37 (0.27), residues: 389 sheet: -1.25 (0.34), residues: 226 loop : -2.11 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 5 HIS 0.006 0.001 HIS B 91 PHE 0.027 0.002 PHE N 108 TYR 0.020 0.002 TYR B 105 ARG 0.004 0.000 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 153 time to evaluate : 0.944 Fit side-chains revert: symmetry clash REVERT: A 291 LEU cc_start: 0.7848 (mp) cc_final: 0.7566 (mp) REVERT: R 199 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7262 (mm) outliers start: 33 outliers final: 19 residues processed: 171 average time/residue: 0.2152 time to fit residues: 49.6489 Evaluate side-chains 165 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 145 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 150 ARG Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 340 THR Chi-restraints excluded: chain R residue 365 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 83 optimal weight: 0.0270 chunk 67 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 0.0370 chunk 87 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 overall best weight: 0.8118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN N 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8409 Z= 0.166 Angle : 0.580 9.833 11379 Z= 0.306 Chirality : 0.043 0.173 1287 Planarity : 0.004 0.042 1445 Dihedral : 4.919 42.637 1133 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.34 % Allowed : 18.91 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.26), residues: 1021 helix: 0.79 (0.27), residues: 386 sheet: -0.96 (0.34), residues: 224 loop : -1.86 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 5 HIS 0.002 0.001 HIS A 357 PHE 0.016 0.001 PHE A 363 TYR 0.015 0.001 TYR R 176 ARG 0.004 0.000 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 153 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 291 LEU cc_start: 0.7670 (mp) cc_final: 0.7431 (mp) REVERT: A 380 ARG cc_start: 0.6767 (mtp85) cc_final: 0.6140 (mtp85) REVERT: G 48 ASP cc_start: 0.7779 (t70) cc_final: 0.7429 (p0) REVERT: R 105 LYS cc_start: 0.4735 (mttm) cc_final: 0.4272 (mptt) REVERT: R 199 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7198 (mm) outliers start: 30 outliers final: 18 residues processed: 166 average time/residue: 0.2280 time to fit residues: 50.1809 Evaluate side-chains 166 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 147 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain R residue 150 ARG Chi-restraints excluded: chain R residue 153 GLN Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 340 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 0.0170 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 overall best weight: 2.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 268 ASN B 295 ASN G 18 GLN N 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6571 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8409 Z= 0.252 Angle : 0.640 7.997 11379 Z= 0.334 Chirality : 0.044 0.168 1287 Planarity : 0.004 0.044 1445 Dihedral : 5.165 45.753 1133 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.67 % Allowed : 20.02 % Favored : 76.31 % 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: -1.03 (0.26), residues: 1021 helix: 0.68 (0.27), residues: 388 sheet: -0.98 (0.34), residues: 218 loop : -1.80 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 5 HIS 0.005 0.001 HIS B 91 PHE 0.022 0.002 PHE N 108 TYR 0.019 0.002 TYR R 176 ARG 0.003 0.000 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 156 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 380 ARG cc_start: 0.6919 (mtp85) cc_final: 0.6704 (mtp-110) REVERT: G 48 ASP cc_start: 0.7796 (t70) cc_final: 0.7576 (p0) REVERT: N 76 LYS cc_start: 0.7201 (mmtm) cc_final: 0.6744 (mmmt) REVERT: R 105 LYS cc_start: 0.4962 (mttm) cc_final: 0.4435 (mptt) REVERT: R 199 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7188 (mm) outliers start: 33 outliers final: 25 residues processed: 171 average time/residue: 0.2109 time to fit residues: 48.7376 Evaluate side-chains 177 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 151 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 150 ARG Chi-restraints excluded: chain R residue 153 GLN Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 318 ILE Chi-restraints excluded: chain R residue 340 THR Chi-restraints excluded: chain R residue 365 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 chunk 60 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN N 120 GLN R 202 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6571 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 8409 Z= 0.253 Angle : 0.661 9.211 11379 Z= 0.344 Chirality : 0.044 0.151 1287 Planarity : 0.004 0.043 1445 Dihedral : 5.217 45.885 1133 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.67 % Allowed : 21.13 % Favored : 75.19 % 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: -1.10 (0.26), residues: 1021 helix: 0.58 (0.27), residues: 387 sheet: -0.92 (0.35), residues: 213 loop : -1.84 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 5 HIS 0.005 0.001 HIS B 91 PHE 0.023 0.002 PHE R 198 TYR 0.018 0.002 TYR B 105 ARG 0.003 0.000 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 149 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.6996 (mp0) REVERT: A 380 ARG cc_start: 0.6849 (mtp85) cc_final: 0.6511 (mtp-110) REVERT: G 48 ASP cc_start: 0.7757 (t70) cc_final: 0.7539 (p0) REVERT: N 76 LYS cc_start: 0.7199 (mmtm) cc_final: 0.6774 (mmmt) REVERT: R 105 LYS cc_start: 0.4917 (mttm) cc_final: 0.4405 (mptt) REVERT: R 199 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7114 (mm) outliers start: 33 outliers final: 29 residues processed: 162 average time/residue: 0.2310 time to fit residues: 50.0338 Evaluate side-chains 179 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 148 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 150 ARG Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 312 ILE Chi-restraints excluded: chain R residue 318 ILE Chi-restraints excluded: chain R residue 340 THR Chi-restraints excluded: chain R residue 365 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 66 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 9 optimal weight: 0.0970 chunk 76 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 GLN ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6458 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8409 Z= 0.157 Angle : 0.602 8.203 11379 Z= 0.309 Chirality : 0.042 0.162 1287 Planarity : 0.004 0.045 1445 Dihedral : 4.797 43.722 1133 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.23 % Allowed : 22.25 % Favored : 74.53 % 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: -0.68 (0.27), residues: 1021 helix: 0.94 (0.27), residues: 386 sheet: -0.43 (0.37), residues: 198 loop : -1.75 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 209 HIS 0.004 0.001 HIS A 357 PHE 0.026 0.001 PHE R 198 TYR 0.015 0.001 TYR R 176 ARG 0.004 0.000 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 157 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6873 (mp0) REVERT: A 380 ARG cc_start: 0.6620 (mtp85) cc_final: 0.6146 (mtp85) REVERT: G 48 ASP cc_start: 0.7693 (t70) cc_final: 0.7363 (p0) REVERT: N 76 LYS cc_start: 0.7136 (mmtm) cc_final: 0.6770 (mmmt) REVERT: R 105 LYS cc_start: 0.4825 (mttm) cc_final: 0.4317 (mptt) REVERT: R 199 LEU cc_start: 0.7595 (mm) cc_final: 0.7030 (mm) outliers start: 29 outliers final: 22 residues processed: 170 average time/residue: 0.2267 time to fit residues: 51.2047 Evaluate side-chains 176 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 153 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 150 ARG Chi-restraints excluded: chain R residue 153 GLN Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 340 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 8409 Z= 0.307 Angle : 0.705 8.646 11379 Z= 0.365 Chirality : 0.046 0.156 1287 Planarity : 0.004 0.043 1445 Dihedral : 5.289 46.305 1133 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.34 % Allowed : 22.58 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.26), residues: 1021 helix: 0.51 (0.27), residues: 387 sheet: -0.66 (0.37), residues: 197 loop : -1.87 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP B 82 HIS 0.006 0.001 HIS B 91 PHE 0.029 0.002 PHE R 198 TYR 0.019 0.002 TYR B 105 ARG 0.005 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 154 time to evaluate : 0.892 Fit side-chains revert: symmetry clash REVERT: A 344 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7127 (mp0) REVERT: A 380 ARG cc_start: 0.6764 (mtp85) cc_final: 0.6432 (mtp-110) REVERT: A 385 ARG cc_start: 0.7254 (ttm170) cc_final: 0.6959 (ttp-170) REVERT: G 48 ASP cc_start: 0.7760 (t70) cc_final: 0.7400 (p0) REVERT: N 76 LYS cc_start: 0.7220 (mmtm) cc_final: 0.6872 (mmmt) REVERT: R 105 LYS cc_start: 0.5000 (mttm) cc_final: 0.4472 (mptt) REVERT: R 199 LEU cc_start: 0.7749 (mm) cc_final: 0.7161 (mm) outliers start: 30 outliers final: 26 residues processed: 167 average time/residue: 0.2256 time to fit residues: 49.8711 Evaluate side-chains 178 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 151 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 150 ARG Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 312 ILE Chi-restraints excluded: chain R residue 318 ILE Chi-restraints excluded: chain R residue 340 THR Chi-restraints excluded: chain R residue 365 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6533 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8409 Z= 0.211 Angle : 0.648 9.358 11379 Z= 0.334 Chirality : 0.043 0.160 1287 Planarity : 0.004 0.044 1445 Dihedral : 5.052 45.389 1133 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.89 % Allowed : 23.25 % Favored : 73.86 % 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: -0.91 (0.27), residues: 1021 helix: 0.71 (0.27), residues: 384 sheet: -0.66 (0.36), residues: 207 loop : -1.79 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.030 0.002 PHE R 198 TYR 0.016 0.001 TYR R 176 ARG 0.006 0.000 ARG A 228 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 151 time to evaluate : 0.936 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.2740 (ppp) cc_final: 0.2177 (tmm) REVERT: A 344 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7099 (mp0) REVERT: A 380 ARG cc_start: 0.6731 (mtp85) cc_final: 0.6239 (mtp85) REVERT: G 48 ASP cc_start: 0.7722 (t70) cc_final: 0.7359 (p0) REVERT: N 76 LYS cc_start: 0.7215 (mmtm) cc_final: 0.6854 (mmmt) REVERT: R 105 LYS cc_start: 0.4819 (mttm) cc_final: 0.4371 (mptt) REVERT: R 199 LEU cc_start: 0.7808 (mm) cc_final: 0.7230 (mm) outliers start: 26 outliers final: 24 residues processed: 160 average time/residue: 0.2218 time to fit residues: 47.1301 Evaluate side-chains 173 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 148 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 150 ARG Chi-restraints excluded: chain R residue 165 THR Chi-restraints excluded: chain R residue 318 ILE Chi-restraints excluded: chain R residue 340 THR Chi-restraints excluded: chain R residue 350 THR Chi-restraints excluded: chain R residue 365 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 70 optimal weight: 9.9990 chunk 4 optimal weight: 0.2980 chunk 57 optimal weight: 10.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.239007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.207211 restraints weight = 9059.297| |-----------------------------------------------------------------------------| r_work (start): 0.4535 rms_B_bonded: 2.42 r_work: 0.4383 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.4383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6617 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8409 Z= 0.192 Angle : 0.639 9.859 11379 Z= 0.328 Chirality : 0.043 0.158 1287 Planarity : 0.004 0.044 1445 Dihedral : 4.879 45.226 1133 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.11 % Allowed : 23.69 % Favored : 73.19 % 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: -0.82 (0.27), residues: 1021 helix: 0.81 (0.27), residues: 385 sheet: -0.59 (0.36), residues: 207 loop : -1.77 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.015 0.001 PHE R 198 TYR 0.016 0.001 TYR R 176 ARG 0.007 0.000 ARG A 228 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2034.67 seconds wall clock time: 36 minutes 56.00 seconds (2216.00 seconds total)