Starting phenix.real_space_refine on Fri Dec 8 11:38:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xou_33359/12_2023/7xou_33359_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xou_33359/12_2023/7xou_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_33359/12_2023/7xou_33359.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xou_33359/12_2023/7xou_33359.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xou_33359/12_2023/7xou_33359_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xou_33359/12_2023/7xou_33359_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 8247 Number of models: 1 Model: "" Number of chains: 6 Chain: "L" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'NH2': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, '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: "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: 4.73, per 1000 atoms: 0.57 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=0, symmetry=0 Time building additional restraints: 3.07 Conformation dependent library (CDL) restraints added in 2.0 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... running ksdssp... Secondary structure from input PDB file: 25 helices and 11 sheets defined 36.5% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 13 through 37 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 53 through 58 Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.724A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 389 removed outlier: 4.499A pdb=" N ASN A 377 " --> pdb=" O ARG A 374 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLN A 384 " --> pdb=" O ASP A 381 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ARG A 385 " --> pdb=" O ILE A 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'G' and resid 8 through 21 removed outlier: 5.196A pdb=" N ARG G 13 " --> pdb=" O ALA G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 47 removed outlier: 3.817A pdb=" N ALA G 45 " --> pdb=" O CYS G 41 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N GLU G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 44 through 68 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) Processing helix chain 'R' and resid 75 through 93 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 96 through 104 Proline residue: R 101 - end of helix Processing helix chain 'R' and resid 111 through 143 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 155 through 172 Processing helix chain 'R' and resid 203 through 217 Processing helix chain 'R' and resid 220 through 243 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 338 Proline residue: R 328 - end of helix Processing helix chain 'R' and resid 350 through 369 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 376 through 384 removed outlier: 3.853A pdb=" N ALA R 383 " --> pdb=" O LEU R 379 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 286 through 291 removed outlier: 3.670A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id= B, 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: 3.664A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.905A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) 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: 5.676A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.857A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) 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= E, 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= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.977A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (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= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.560A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) 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= H, first strand: chain 'B' and resid 337 through 339 Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'N' and resid 122 through 124 removed outlier: 5.618A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id= K, 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) 366 hydrogen bonds defined for protein. 981 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: 2.22 Time building geometry restraints manager: 3.33 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: 2681 1.34 - 1.46: 1989 1.46 - 1.58: 3647 1.58 - 1.70: 1 1.70 - 1.82: 92 Bond restraints: 8410 Sorted by residual: bond pdb=" C PHE L 8 " pdb=" N NH2 L 9 " ideal model delta sigma weight residual 2.329 1.329 1.000 1.40e-02 5.10e+03 5.10e+03 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 ... (remaining 8405 not shown) Histogram of bond angle deviations from ideal: 99.74 - 106.59: 194 106.59 - 113.45: 4557 113.45 - 120.30: 3179 120.30 - 127.16: 3368 127.16 - 134.01: 83 Bond angle restraints: 11381 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 11376 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: 1446 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 1443 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 790 2.74 - 3.28: 8426 3.28 - 3.82: 13565 3.82 - 4.36: 16403 4.36 - 4.90: 28094 Nonbonded interactions: 67278 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 67273 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: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.930 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 24.960 Find NCS groups from input model: 0.220 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.400 ------------------------------------------------------------------------------- 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 : 0.012 1.000 8410 Z= 0.812 Angle : 0.707 9.794 11381 Z= 0.395 Chirality : 0.045 0.174 1287 Planarity : 0.005 0.047 1446 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 : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 192 average time/residue: 0.2388 time to fit residues: 59.4513 Evaluate side-chains 150 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 0.831 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1852 ------------------------------------------------------------------------------- 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: 0.9980 chunk 76 optimal weight: 0.4980 chunk 42 optimal weight: 0.4980 chunk 26 optimal weight: 5.9990 chunk 51 optimal weight: 0.3980 chunk 40 optimal weight: 9.9990 chunk 79 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN N 120 GLN R 102 ASN R 181 ASN R 194 ASN R 238 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6443 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8410 Z= 0.156 Angle : 0.578 8.291 11381 Z= 0.298 Chirality : 0.042 0.165 1287 Planarity : 0.004 0.048 1446 Dihedral : 4.910 39.951 1133 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.31 % Favored : 95.59 % Rotamer: Outliers : 1.45 % Allowed : 12.90 % Favored : 85.65 % 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: -2.04 (0.25), residues: 1021 helix: -0.24 (0.26), residues: 387 sheet: -1.35 (0.33), residues: 225 loop : -2.38 (0.27), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 5 HIS 0.002 0.001 HIS B 91 PHE 0.018 0.001 PHE R 242 TYR 0.025 0.001 TYR N 60 ARG 0.002 0.000 ARG A 232 *********************** 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 177 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 164 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 169 average time/residue: 0.2209 time to fit residues: 50.0197 Evaluate side-chains 160 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 153 time to evaluate : 0.918 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1612 time to fit residues: 2.9134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 62 optimal weight: 10.0000 chunk 25 optimal weight: 0.0070 chunk 91 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 overall best weight: 1.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 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: 0.6523 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8410 Z= 0.208 Angle : 0.605 8.977 11381 Z= 0.314 Chirality : 0.043 0.155 1287 Planarity : 0.005 0.049 1446 Dihedral : 5.017 43.176 1133 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.56 % Allowed : 16.02 % Favored : 82.42 % 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: -1.64 (0.26), residues: 1021 helix: 0.13 (0.27), residues: 383 sheet: -1.06 (0.33), residues: 230 loop : -2.24 (0.28), residues: 408 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 0.018 0.002 PHE R 107 TYR 0.018 0.002 TYR R 176 ARG 0.002 0.000 ARG B 129 *********************** 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 169 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 155 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 163 average time/residue: 0.2234 time to fit residues: 48.8494 Evaluate side-chains 151 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 144 time to evaluate : 0.819 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0798 time to fit residues: 2.1791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 chunk 92 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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** B 6 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN R 102 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6475 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8410 Z= 0.171 Angle : 0.579 10.191 11381 Z= 0.302 Chirality : 0.042 0.152 1287 Planarity : 0.005 0.052 1446 Dihedral : 4.805 41.172 1133 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.70 % Favored : 95.20 % Rotamer: Outliers : 1.45 % Allowed : 18.80 % Favored : 79.76 % 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: -1.20 (0.26), residues: 1021 helix: 0.48 (0.28), residues: 379 sheet: -0.77 (0.34), residues: 230 loop : -2.00 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 5 HIS 0.004 0.001 HIS A 387 PHE 0.020 0.001 PHE A 376 TYR 0.017 0.001 TYR R 176 ARG 0.003 0.000 ARG A 228 *********************** 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 161 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 148 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 156 average time/residue: 0.2236 time to fit residues: 46.7032 Evaluate side-chains 147 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 141 time to evaluate : 0.906 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2384 time to fit residues: 3.2021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 72 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 83 optimal weight: 0.0020 chunk 67 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 overall best weight: 4.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN N 39 GLN N 120 GLN ** R 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 8410 Z= 0.440 Angle : 0.787 8.735 11381 Z= 0.411 Chirality : 0.050 0.164 1287 Planarity : 0.006 0.061 1446 Dihedral : 5.840 49.914 1133 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.42 % Favored : 91.38 % Rotamer: Outliers : 3.00 % Allowed : 19.02 % Favored : 77.98 % 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: -1.95 (0.25), residues: 1021 helix: -0.41 (0.26), residues: 385 sheet: -1.13 (0.34), residues: 230 loop : -2.18 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP L 5 HIS 0.012 0.002 HIS B 91 PHE 0.038 0.003 PHE R 377 TYR 0.030 0.003 TYR B 105 ARG 0.004 0.001 ARG N 67 *********************** 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 173 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 146 time to evaluate : 0.848 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 17 residues processed: 161 average time/residue: 0.2268 time to fit residues: 48.7872 Evaluate side-chains 157 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 140 time to evaluate : 0.933 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0782 time to fit residues: 3.6421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6555 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 8410 Z= 0.210 Angle : 0.619 7.780 11381 Z= 0.325 Chirality : 0.043 0.149 1287 Planarity : 0.005 0.064 1446 Dihedral : 5.156 45.300 1133 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.68 % Favored : 94.22 % Rotamer: Outliers : 1.45 % Allowed : 21.02 % Favored : 77.53 % 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: -1.33 (0.26), residues: 1021 helix: 0.11 (0.27), residues: 388 sheet: -0.71 (0.35), residues: 224 loop : -1.90 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 209 HIS 0.005 0.001 HIS B 91 PHE 0.018 0.002 PHE A 363 TYR 0.016 0.001 TYR R 176 ARG 0.004 0.000 ARG B 19 *********************** 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 161 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 148 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 155 average time/residue: 0.2239 time to fit residues: 47.0055 Evaluate side-chains 141 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 136 time to evaluate : 1.020 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1003 time to fit residues: 2.1430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 71 optimal weight: 0.0060 chunk 82 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 97 optimal weight: 0.2980 chunk 60 optimal weight: 0.2980 chunk 59 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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** ** 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: 0.6450 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8410 Z= 0.157 Angle : 0.586 8.066 11381 Z= 0.309 Chirality : 0.042 0.160 1287 Planarity : 0.005 0.071 1446 Dihedral : 4.721 43.570 1133 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.70 % Favored : 95.20 % Rotamer: Outliers : 0.67 % Allowed : 22.47 % Favored : 76.86 % 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: -0.88 (0.26), residues: 1021 helix: 0.61 (0.28), residues: 378 sheet: -0.44 (0.35), residues: 220 loop : -1.74 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 209 HIS 0.003 0.001 HIS A 220 PHE 0.032 0.001 PHE R 198 TYR 0.016 0.001 TYR R 176 ARG 0.003 0.000 ARG B 19 *********************** 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 147 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 141 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 145 average time/residue: 0.2350 time to fit residues: 45.3675 Evaluate side-chains 139 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 134 time to evaluate : 0.915 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0869 time to fit residues: 2.0652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN N 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6492 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8410 Z= 0.192 Angle : 0.611 11.508 11381 Z= 0.322 Chirality : 0.042 0.152 1287 Planarity : 0.005 0.073 1446 Dihedral : 4.805 45.475 1133 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.60 % Favored : 95.30 % Rotamer: Outliers : 0.44 % Allowed : 23.14 % Favored : 76.42 % 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: -0.83 (0.27), residues: 1021 helix: 0.60 (0.28), residues: 379 sheet: -0.36 (0.35), residues: 218 loop : -1.69 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 339 HIS 0.003 0.001 HIS B 91 PHE 0.029 0.002 PHE R 198 TYR 0.017 0.001 TYR N 60 ARG 0.006 0.000 ARG A 228 *********************** 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 143 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 139 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 143 average time/residue: 0.2472 time to fit residues: 46.9376 Evaluate side-chains 134 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 133 time to evaluate : 0.898 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0860 time to fit residues: 1.5494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 5.9990 chunk 93 optimal weight: 0.5980 chunk 54 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 27 optimal weight: 0.0970 chunk 81 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 59 optimal weight: 0.3980 chunk 95 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6419 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8410 Z= 0.157 Angle : 0.582 8.466 11381 Z= 0.304 Chirality : 0.042 0.153 1287 Planarity : 0.005 0.074 1446 Dihedral : 4.531 42.934 1133 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.53 % Favored : 96.38 % Rotamer: Outliers : 0.33 % Allowed : 24.03 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.27), residues: 1021 helix: 0.78 (0.28), residues: 379 sheet: -0.20 (0.35), residues: 218 loop : -1.62 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 339 HIS 0.002 0.001 HIS A 357 PHE 0.029 0.001 PHE R 198 TYR 0.017 0.001 TYR R 176 ARG 0.006 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 146 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 143 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 143 average time/residue: 0.2442 time to fit residues: 46.1708 Evaluate side-chains 132 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 131 time to evaluate : 0.930 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0761 time to fit residues: 1.4350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8410 Z= 0.252 Angle : 0.652 8.366 11381 Z= 0.341 Chirality : 0.044 0.156 1287 Planarity : 0.005 0.072 1446 Dihedral : 4.926 46.290 1133 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.19 % Favored : 94.71 % Rotamer: Outliers : 0.11 % Allowed : 25.03 % Favored : 74.86 % 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: -0.89 (0.27), residues: 1021 helix: 0.50 (0.27), residues: 385 sheet: -0.31 (0.35), residues: 218 loop : -1.77 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 339 HIS 0.006 0.001 HIS B 91 PHE 0.030 0.002 PHE R 198 TYR 0.019 0.002 TYR B 105 ARG 0.006 0.000 ARG B 129 ********************** 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 134 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 133 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 133 average time/residue: 0.2257 time to fit residues: 40.6635 Evaluate side-chains 131 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 0.938 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0776 time to fit residues: 1.4563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 22 optimal weight: 0.1980 chunk 80 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.0570 chunk 70 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 overall best weight: 1.0302 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4798 r_free = 0.4798 target = 0.241667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.209536 restraints weight = 8907.632| |-----------------------------------------------------------------------------| r_work (start): 0.4561 rms_B_bonded: 2.44 r_work: 0.4409 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8410 Z= 0.186 Angle : 0.631 13.477 11381 Z= 0.328 Chirality : 0.043 0.168 1287 Planarity : 0.005 0.073 1446 Dihedral : 4.783 46.100 1133 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.92 % Favored : 95.98 % Rotamer: Outliers : 0.11 % Allowed : 25.25 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.27), residues: 1021 helix: 0.64 (0.27), residues: 385 sheet: -0.22 (0.36), residues: 208 loop : -1.74 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 339 HIS 0.003 0.001 HIS B 91 PHE 0.031 0.002 PHE R 198 TYR 0.016 0.001 TYR R 360 ARG 0.006 0.000 ARG B 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1971.69 seconds wall clock time: 36 minutes 38.70 seconds (2198.70 seconds total)