Starting phenix.real_space_refine on Mon Mar 11 18:30:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c2e_30274/03_2024/7c2e_30274_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c2e_30274/03_2024/7c2e_30274.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c2e_30274/03_2024/7c2e_30274.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c2e_30274/03_2024/7c2e_30274.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c2e_30274/03_2024/7c2e_30274_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c2e_30274/03_2024/7c2e_30274_neut_updated.pdb" } resolution = 4.2 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= 0.003 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: 5 Type Number sf(0) Gaussians S 53 5.16 5 C 5632 2.51 5 N 1529 2.21 5 O 1613 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 102": "NH1" <-> "NH2" Residue "R TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 310": "NH1" <-> "NH2" Residue "R ARG 326": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8828 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1637 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 6, 'TRANS': 186} Chain breaks: 4 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} 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: 3193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3193 Unusual residues: {'FFR': 1} Classifications: {'peptide': 380, 'undetermined': 1} Link IDs: {'PTRANS': 14, 'TRANS': 365, None: 1} Not linked: pdbres="GLU R 423 " pdbres="FFR R 501 " Chain breaks: 2 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ALA R 209 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA R 209 " occ=0.00 Time building chain proxies: 4.93, per 1000 atoms: 0.56 Number of scatterers: 8828 At special positions: 0 Unit cell: (82.555, 154.66, 121.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 53 16.00 F 1 9.00 O 1613 8.00 N 1529 7.00 C 5632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " 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: 2.99 Conformation dependent library (CDL) restraints added in 1.6 seconds 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2064 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 10 sheets defined 35.2% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 12 through 38 Processing helix chain 'A' and resid 231 through 233 No H-bonds generated for 'chain 'A' and resid 231 through 233' Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 313 through 317 removed outlier: 4.186A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG A 317 " --> pdb=" O GLU A 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 317' Processing helix chain 'A' and resid 332 through 350 Processing helix chain 'A' and resid 372 through 390 Processing helix chain 'B' and resid 5 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 8 through 23 Processing helix chain 'G' and resid 30 through 44 Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'R' and resid 32 through 51 Processing helix chain 'R' and resid 138 through 168 Processing helix chain 'R' and resid 175 through 197 Processing helix chain 'R' and resid 207 through 210 No H-bonds generated for 'chain 'R' and resid 207 through 210' Processing helix chain 'R' and resid 212 through 221 Processing helix chain 'R' and resid 224 through 256 Processing helix chain 'R' and resid 262 through 273 Processing helix chain 'R' and resid 276 through 291 Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 304 through 336 removed outlier: 4.311A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 345 through 359 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 363 through 368 Processing helix chain 'R' and resid 381 through 390 removed outlier: 4.279A pdb=" N GLU R 387 " --> pdb=" O LYS R 383 " (cutoff:3.500A) Processing helix chain 'R' and resid 394 through 404 Processing helix chain 'R' and resid 407 through 422 Processing sheet with id= A, first strand: chain 'A' and resid 360 through 363 removed outlier: 3.745A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 60 through 63 removed outlier: 3.755A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 123 through 125 removed outlier: 3.582A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 7.178A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 209 through 212 removed outlier: 3.897A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 252 through 254 Processing sheet with id= G, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.383A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.819A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA B 328 " --> pdb=" O GLY B 319 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY B 319 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 18 through 23 removed outlier: 3.750A pdb=" N LEU N 18 " --> pdb=" O MET N 83 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 122 through 124 removed outlier: 3.967A pdb=" N THR N 122 " --> pdb=" O TYR N 94 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR N 94 " --> pdb=" O THR N 122 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL N 124 " --> pdb=" O ALA N 92 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA N 92 " --> pdb=" O VAL N 124 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 358 hydrogen bonds defined for protein. 1050 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: 2.24 Time building geometry restraints manager: 3.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1426 1.29 - 1.43: 2516 1.43 - 1.57: 5024 1.57 - 1.70: 0 1.70 - 1.84: 71 Bond restraints: 9037 Sorted by residual: bond pdb=" C21 FFR R 501 " pdb=" N20 FFR R 501 " ideal model delta sigma weight residual 1.306 1.364 -0.058 2.00e-02 2.50e+03 8.43e+00 bond pdb=" C36 FFR R 501 " pdb=" O39 FFR R 501 " ideal model delta sigma weight residual 1.433 1.489 -0.056 2.00e-02 2.50e+03 7.88e+00 bond pdb=" C38 FFR R 501 " pdb=" O39 FFR R 501 " ideal model delta sigma weight residual 1.436 1.490 -0.054 2.00e-02 2.50e+03 7.16e+00 bond pdb=" C LEU R 118 " pdb=" N PRO R 119 " ideal model delta sigma weight residual 1.331 1.359 -0.028 1.20e-02 6.94e+03 5.49e+00 bond pdb=" C21 FFR R 501 " pdb=" O22 FFR R 501 " ideal model delta sigma weight residual 1.341 1.382 -0.041 2.00e-02 2.50e+03 4.14e+00 ... (remaining 9032 not shown) Histogram of bond angle deviations from ideal: 87.25 - 105.66: 149 105.66 - 124.07: 11808 124.07 - 142.48: 294 142.48 - 160.89: 0 160.89 - 179.30: 1 Bond angle restraints: 12252 Sorted by residual: angle pdb=" C ASN R 302 " pdb=" N MET R 303 " pdb=" CA MET R 303 " ideal model delta sigma weight residual 121.54 131.12 -9.58 1.91e+00 2.74e-01 2.52e+01 angle pdb=" N GLY R 361 " pdb=" CA GLY R 361 " pdb=" C GLY R 361 " ideal model delta sigma weight residual 111.03 117.91 -6.88 1.40e+00 5.10e-01 2.42e+01 angle pdb=" CA TYR R 148 " pdb=" CB TYR R 148 " pdb=" CG TYR R 148 " ideal model delta sigma weight residual 113.90 122.47 -8.57 1.80e+00 3.09e-01 2.27e+01 angle pdb=" C LYS N 76 " pdb=" N ASN N 77 " pdb=" CA ASN N 77 " ideal model delta sigma weight residual 121.54 130.57 -9.03 1.91e+00 2.74e-01 2.23e+01 angle pdb=" C THR B 86 " pdb=" N THR B 87 " pdb=" CA THR B 87 " ideal model delta sigma weight residual 121.54 129.72 -8.18 1.91e+00 2.74e-01 1.84e+01 ... (remaining 12247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.00: 5079 15.00 - 30.00: 189 30.00 - 45.00: 59 45.00 - 60.00: 6 60.00 - 75.00: 3 Dihedral angle restraints: 5336 sinusoidal: 2146 harmonic: 3190 Sorted by residual: dihedral pdb=" CA SER R 261 " pdb=" C SER R 261 " pdb=" N GLU R 262 " pdb=" CA GLU R 262 " ideal model delta harmonic sigma weight residual 180.00 -151.27 -28.73 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA ARG R 299 " pdb=" C ARG R 299 " pdb=" N ASN R 300 " pdb=" CA ASN R 300 " ideal model delta harmonic sigma weight residual 180.00 -152.99 -27.01 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA ARG A 228 " pdb=" C ARG A 228 " pdb=" N ASP A 229 " pdb=" CA ASP A 229 " ideal model delta harmonic sigma weight residual 180.00 -157.21 -22.79 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 5333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 932 0.044 - 0.089: 296 0.089 - 0.133: 92 0.133 - 0.177: 15 0.177 - 0.222: 3 Chirality restraints: 1338 Sorted by residual: chirality pdb=" CB THR R 378 " pdb=" CA THR R 378 " pdb=" OG1 THR R 378 " pdb=" CG2 THR R 378 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA ASN N 77 " pdb=" N ASN N 77 " pdb=" C ASN N 77 " pdb=" CB ASN N 77 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA THR B 87 " pdb=" N THR B 87 " pdb=" C THR B 87 " pdb=" CB THR B 87 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.33e-01 ... (remaining 1335 not shown) Planarity restraints: 1556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C02 FFR R 501 " -0.146 2.00e-02 2.50e+03 8.09e-02 1.96e+02 pdb=" C04 FFR R 501 " -0.018 2.00e-02 2.50e+03 pdb=" C06 FFR R 501 " 0.033 2.00e-02 2.50e+03 pdb=" C07 FFR R 501 " 0.038 2.00e-02 2.50e+03 pdb=" C08 FFR R 501 " 0.060 2.00e-02 2.50e+03 pdb=" C09 FFR R 501 " 0.040 2.00e-02 2.50e+03 pdb=" C11 FFR R 501 " -0.025 2.00e-02 2.50e+03 pdb=" C12 FFR R 501 " -0.177 2.00e-02 2.50e+03 pdb=" C35 FFR R 501 " 0.120 2.00e-02 2.50e+03 pdb=" N1 FFR R 501 " 0.010 2.00e-02 2.50e+03 pdb=" N10 FFR R 501 " 0.014 2.00e-02 2.50e+03 pdb=" N34 FFR R 501 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 FFR R 501 " -0.020 2.00e-02 2.50e+03 5.18e-02 6.72e+01 pdb=" C23 FFR R 501 " -0.118 2.00e-02 2.50e+03 pdb=" C24 FFR R 501 " 0.011 2.00e-02 2.50e+03 pdb=" C25 FFR R 501 " 0.042 2.00e-02 2.50e+03 pdb=" C26 FFR R 501 " 0.052 2.00e-02 2.50e+03 pdb=" C28 FFR R 501 " 0.030 2.00e-02 2.50e+03 pdb=" C29 FFR R 501 " 0.025 2.00e-02 2.50e+03 pdb=" C30 FFR R 501 " 0.027 2.00e-02 2.50e+03 pdb=" F1 FFR R 501 " 0.022 2.00e-02 2.50e+03 pdb=" N2 FFR R 501 " -0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET R 303 " 0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C MET R 303 " -0.056 2.00e-02 2.50e+03 pdb=" O MET R 303 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN R 304 " 0.019 2.00e-02 2.50e+03 ... (remaining 1553 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 94 2.64 - 3.20: 7266 3.20 - 3.77: 13486 3.77 - 4.33: 17792 4.33 - 4.90: 29443 Nonbonded interactions: 68081 Sorted by model distance: nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.071 2.440 nonbonded pdb=" ND1 HIS G 44 " pdb=" OE2 GLU G 47 " model vdw 2.182 2.520 nonbonded pdb=" OD2 ASP R 67 " pdb=" NH2 ARG R 102 " model vdw 2.198 2.520 nonbonded pdb=" OG1 THR B 184 " pdb=" OD2 ASP B 205 " model vdw 2.243 2.440 nonbonded pdb=" NZ LYS A 233 " pdb=" OD2 ASP B 228 " model vdw 2.261 2.520 ... (remaining 68076 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.400 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: 2.240 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 25.370 Find NCS groups from input model: 0.240 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: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 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 0.058 9037 Z= 0.229 Angle : 0.797 9.579 12252 Z= 0.450 Chirality : 0.049 0.222 1338 Planarity : 0.007 0.081 1556 Dihedral : 9.286 75.003 3254 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.21), residues: 1072 helix: -1.26 (0.19), residues: 396 sheet: -2.87 (0.33), residues: 169 loop : -2.79 (0.23), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 274 HIS 0.006 0.001 HIS R 171 PHE 0.023 0.002 PHE R 413 TYR 0.030 0.002 TYR R 178 ARG 0.004 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 488 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 GLN cc_start: 0.8144 (tp40) cc_final: 0.7787 (tp40) REVERT: A 270 LEU cc_start: 0.9027 (mt) cc_final: 0.8824 (mt) REVERT: A 272 LEU cc_start: 0.9148 (tp) cc_final: 0.8748 (tp) REVERT: A 279 ASN cc_start: 0.7763 (t0) cc_final: 0.7495 (t0) REVERT: A 386 MET cc_start: 0.8142 (tmt) cc_final: 0.7368 (tmm) REVERT: A 390 GLN cc_start: 0.8595 (mt0) cc_final: 0.7657 (mm-40) REVERT: B 16 ASN cc_start: 0.8537 (m-40) cc_final: 0.8285 (m-40) REVERT: B 75 GLN cc_start: 0.8596 (mp-120) cc_final: 0.8366 (mp10) REVERT: B 76 ASP cc_start: 0.7059 (p0) cc_final: 0.6645 (t0) REVERT: B 101 MET cc_start: 0.7700 (mtp) cc_final: 0.7389 (mtm) REVERT: B 253 PHE cc_start: 0.8089 (m-80) cc_final: 0.7773 (m-80) REVERT: B 276 VAL cc_start: 0.9110 (m) cc_final: 0.8642 (m) REVERT: B 308 LEU cc_start: 0.8689 (mt) cc_final: 0.8349 (mp) REVERT: N 122 THR cc_start: 0.5617 (p) cc_final: 0.4983 (p) REVERT: R 34 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8118 (tp30) REVERT: R 37 GLN cc_start: 0.8986 (mm-40) cc_final: 0.8448 (tm-30) REVERT: R 38 LYS cc_start: 0.9182 (mttt) cc_final: 0.8912 (mttt) REVERT: R 67 ASP cc_start: 0.7810 (p0) cc_final: 0.7156 (p0) REVERT: R 69 TYR cc_start: 0.7985 (t80) cc_final: 0.7562 (t80) REVERT: R 163 SER cc_start: 0.9229 (m) cc_final: 0.8883 (p) REVERT: R 179 ILE cc_start: 0.9293 (mm) cc_final: 0.8930 (mm) REVERT: R 230 PHE cc_start: 0.7746 (t80) cc_final: 0.7087 (t80) REVERT: R 303 MET cc_start: 0.6550 (tpp) cc_final: 0.5964 (tpp) REVERT: R 387 GLU cc_start: 0.8467 (tm-30) cc_final: 0.7954 (mt-10) REVERT: R 393 PHE cc_start: 0.7554 (m-10) cc_final: 0.6919 (m-10) outliers start: 0 outliers final: 0 residues processed: 488 average time/residue: 0.2460 time to fit residues: 155.3513 Evaluate side-chains 264 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 32 optimal weight: 20.0000 chunk 50 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 74 ASN R 171 HIS R 177 ASN R 180 HIS R 240 ASN R 394 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.5004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9037 Z= 0.277 Angle : 0.680 12.991 12252 Z= 0.353 Chirality : 0.044 0.163 1338 Planarity : 0.005 0.044 1556 Dihedral : 5.409 50.235 1220 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.21 % Allowed : 4.33 % Favored : 95.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.24), residues: 1072 helix: 0.48 (0.25), residues: 411 sheet: -2.26 (0.36), residues: 174 loop : -2.36 (0.25), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 284 HIS 0.008 0.002 HIS B 225 PHE 0.017 0.002 PHE A 273 TYR 0.018 0.002 TYR R 242 ARG 0.009 0.001 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 323 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 THR cc_start: 0.8259 (m) cc_final: 0.7703 (m) REVERT: A 270 LEU cc_start: 0.9091 (mt) cc_final: 0.8846 (mt) REVERT: A 389 ARG cc_start: 0.7753 (ppt170) cc_final: 0.7269 (ppt170) REVERT: A 390 GLN cc_start: 0.8882 (mt0) cc_final: 0.7794 (mm-40) REVERT: B 16 ASN cc_start: 0.8511 (m-40) cc_final: 0.8272 (m-40) REVERT: B 76 ASP cc_start: 0.7858 (p0) cc_final: 0.7149 (t0) REVERT: B 146 LEU cc_start: 0.8779 (mp) cc_final: 0.8016 (mp) REVERT: B 308 LEU cc_start: 0.8896 (mt) cc_final: 0.8677 (mt) REVERT: B 311 HIS cc_start: 0.5499 (m-70) cc_final: 0.4816 (m-70) REVERT: B 337 LYS cc_start: 0.8879 (mptt) cc_final: 0.8194 (mptt) REVERT: G 20 LYS cc_start: 0.7722 (pptt) cc_final: 0.7113 (tptt) REVERT: N 18 LEU cc_start: 0.8458 (tp) cc_final: 0.8020 (tp) REVERT: N 20 LEU cc_start: 0.8497 (mt) cc_final: 0.8255 (mt) REVERT: N 83 MET cc_start: 0.7812 (mtm) cc_final: 0.7392 (mtm) REVERT: N 120 GLN cc_start: 0.6884 (pp30) cc_final: 0.6673 (pp30) REVERT: R 37 GLN cc_start: 0.9132 (mm-40) cc_final: 0.8422 (tm-30) REVERT: R 44 ARG cc_start: 0.9229 (tmt170) cc_final: 0.8910 (tpt90) REVERT: R 67 ASP cc_start: 0.8159 (p0) cc_final: 0.7138 (p0) REVERT: R 163 SER cc_start: 0.9324 (m) cc_final: 0.8990 (p) REVERT: R 179 ILE cc_start: 0.9142 (mm) cc_final: 0.8579 (mm) REVERT: R 181 LEU cc_start: 0.9308 (tp) cc_final: 0.9079 (tp) REVERT: R 184 PHE cc_start: 0.8313 (m-10) cc_final: 0.7923 (m-10) REVERT: R 230 PHE cc_start: 0.8341 (t80) cc_final: 0.7676 (t80) REVERT: R 246 VAL cc_start: 0.9358 (t) cc_final: 0.9115 (p) REVERT: R 415 LYS cc_start: 0.8961 (ptpp) cc_final: 0.8441 (ptpp) outliers start: 2 outliers final: 0 residues processed: 323 average time/residue: 0.2273 time to fit residues: 98.3051 Evaluate side-chains 229 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 78 optimal weight: 0.0040 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 HIS ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 HIS B 340 ASN R 171 HIS R 407 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.5421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9037 Z= 0.169 Angle : 0.590 10.557 12252 Z= 0.305 Chirality : 0.042 0.136 1338 Planarity : 0.004 0.032 1556 Dihedral : 5.046 37.701 1220 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % 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: -1.32 (0.25), residues: 1072 helix: 1.00 (0.26), residues: 406 sheet: -2.04 (0.37), residues: 181 loop : -2.08 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP R 284 HIS 0.008 0.001 HIS B 54 PHE 0.016 0.001 PHE B 253 TYR 0.016 0.002 TYR R 305 ARG 0.004 0.000 ARG R 190 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 LEU cc_start: 0.8931 (tp) cc_final: 0.8700 (tp) REVERT: A 272 LEU cc_start: 0.9288 (tp) cc_final: 0.8845 (tp) REVERT: A 349 SER cc_start: 0.8594 (t) cc_final: 0.8327 (p) REVERT: A 386 MET cc_start: 0.7944 (tmm) cc_final: 0.7299 (tmm) REVERT: A 389 ARG cc_start: 0.7672 (ppt170) cc_final: 0.7226 (ppt170) REVERT: A 390 GLN cc_start: 0.8823 (mt0) cc_final: 0.7970 (mm-40) REVERT: B 16 ASN cc_start: 0.8552 (m-40) cc_final: 0.8282 (m-40) REVERT: B 50 THR cc_start: 0.8062 (m) cc_final: 0.7709 (p) REVERT: B 76 ASP cc_start: 0.7994 (p0) cc_final: 0.7126 (t70) REVERT: B 262 MET cc_start: 0.7797 (ttm) cc_final: 0.7596 (ttm) REVERT: B 308 LEU cc_start: 0.8829 (mt) cc_final: 0.7616 (mt) REVERT: B 337 LYS cc_start: 0.8830 (mptt) cc_final: 0.8340 (mptt) REVERT: B 339 TRP cc_start: 0.7200 (m100) cc_final: 0.6852 (m-10) REVERT: G 20 LYS cc_start: 0.7786 (pptt) cc_final: 0.7302 (tptt) REVERT: G 37 LEU cc_start: 0.8877 (mt) cc_final: 0.8455 (pp) REVERT: N 18 LEU cc_start: 0.8309 (tp) cc_final: 0.8062 (tp) REVERT: N 83 MET cc_start: 0.7801 (mtm) cc_final: 0.7451 (mtm) REVERT: N 122 THR cc_start: 0.4324 (p) cc_final: 0.4055 (p) REVERT: R 37 GLN cc_start: 0.9164 (mm-40) cc_final: 0.8630 (tm-30) REVERT: R 67 ASP cc_start: 0.8049 (p0) cc_final: 0.7002 (p0) REVERT: R 163 SER cc_start: 0.9325 (m) cc_final: 0.9039 (p) REVERT: R 179 ILE cc_start: 0.9071 (mm) cc_final: 0.8676 (mm) REVERT: R 184 PHE cc_start: 0.8185 (m-10) cc_final: 0.7914 (m-10) REVERT: R 230 PHE cc_start: 0.8324 (t80) cc_final: 0.7680 (t80) REVERT: R 414 ARG cc_start: 0.8040 (mmt180) cc_final: 0.7786 (mmt180) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.2011 time to fit residues: 84.1912 Evaluate side-chains 236 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN R 171 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.5691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9037 Z= 0.160 Angle : 0.572 8.123 12252 Z= 0.298 Chirality : 0.041 0.141 1338 Planarity : 0.003 0.032 1556 Dihedral : 4.881 37.273 1220 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % 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 (0.25), residues: 1072 helix: 1.08 (0.26), residues: 403 sheet: -1.72 (0.37), residues: 182 loop : -1.89 (0.26), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 284 HIS 0.008 0.001 HIS R 173 PHE 0.012 0.001 PHE B 151 TYR 0.017 0.002 TYR R 220 ARG 0.002 0.000 ARG R 43 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 ASP cc_start: 0.6909 (t0) cc_final: 0.6429 (t0) REVERT: A 270 LEU cc_start: 0.9051 (mt) cc_final: 0.8842 (mt) REVERT: A 272 LEU cc_start: 0.9268 (tp) cc_final: 0.8821 (tp) REVERT: A 284 ASP cc_start: 0.7639 (m-30) cc_final: 0.7409 (m-30) REVERT: A 386 MET cc_start: 0.7958 (tmm) cc_final: 0.7284 (tmm) REVERT: A 389 ARG cc_start: 0.7730 (ppt170) cc_final: 0.7316 (ppt170) REVERT: A 390 GLN cc_start: 0.8949 (mt0) cc_final: 0.8283 (mm-40) REVERT: B 16 ASN cc_start: 0.8549 (m-40) cc_final: 0.8266 (m-40) REVERT: B 52 ARG cc_start: 0.7518 (mpp80) cc_final: 0.7201 (ptm160) REVERT: B 76 ASP cc_start: 0.7996 (p0) cc_final: 0.7102 (t0) REVERT: B 252 LEU cc_start: 0.9461 (tp) cc_final: 0.9241 (tp) REVERT: B 308 LEU cc_start: 0.8880 (mt) cc_final: 0.7647 (mp) REVERT: B 337 LYS cc_start: 0.8827 (mptt) cc_final: 0.8289 (mptt) REVERT: B 339 TRP cc_start: 0.7209 (m100) cc_final: 0.6791 (m-10) REVERT: G 20 LYS cc_start: 0.7953 (pptt) cc_final: 0.7487 (tptt) REVERT: N 18 LEU cc_start: 0.8201 (tp) cc_final: 0.7826 (tp) REVERT: N 20 LEU cc_start: 0.8513 (mt) cc_final: 0.8197 (mt) REVERT: N 77 ASN cc_start: 0.7891 (t0) cc_final: 0.7162 (t0) REVERT: N 83 MET cc_start: 0.7824 (mtm) cc_final: 0.7480 (mtm) REVERT: R 37 GLN cc_start: 0.9144 (mm-40) cc_final: 0.8680 (tm-30) REVERT: R 38 LYS cc_start: 0.9186 (pttm) cc_final: 0.8734 (pttt) REVERT: R 67 ASP cc_start: 0.8058 (p0) cc_final: 0.6913 (p0) REVERT: R 163 SER cc_start: 0.9307 (m) cc_final: 0.9044 (p) REVERT: R 184 PHE cc_start: 0.8169 (m-10) cc_final: 0.7916 (m-10) REVERT: R 230 PHE cc_start: 0.8288 (t80) cc_final: 0.7890 (t80) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.1955 time to fit residues: 79.9668 Evaluate side-chains 221 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 77 optimal weight: 20.0000 chunk 42 optimal weight: 6.9990 chunk 88 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 52 optimal weight: 0.4980 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 171 HIS R 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.6258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9037 Z= 0.229 Angle : 0.619 8.398 12252 Z= 0.326 Chirality : 0.042 0.144 1338 Planarity : 0.004 0.036 1556 Dihedral : 5.152 46.568 1220 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % 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: -0.87 (0.26), residues: 1072 helix: 1.15 (0.26), residues: 404 sheet: -1.45 (0.38), residues: 184 loop : -1.73 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 99 HIS 0.009 0.002 HIS B 225 PHE 0.021 0.002 PHE A 273 TYR 0.017 0.002 TYR B 105 ARG 0.004 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 288 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 THR cc_start: 0.8543 (m) cc_final: 0.8262 (m) REVERT: A 223 ASP cc_start: 0.7333 (t0) cc_final: 0.6803 (t70) REVERT: A 270 LEU cc_start: 0.9092 (mt) cc_final: 0.8847 (mt) REVERT: A 272 LEU cc_start: 0.9359 (tp) cc_final: 0.9016 (tp) REVERT: A 279 ASN cc_start: 0.7544 (t0) cc_final: 0.7332 (t0) REVERT: A 346 LEU cc_start: 0.8924 (mt) cc_final: 0.8711 (mt) REVERT: A 386 MET cc_start: 0.7999 (tmm) cc_final: 0.7270 (tmm) REVERT: A 389 ARG cc_start: 0.7722 (ppt170) cc_final: 0.7308 (ppt170) REVERT: A 390 GLN cc_start: 0.9001 (mt0) cc_final: 0.8223 (mm-40) REVERT: B 16 ASN cc_start: 0.8630 (m-40) cc_final: 0.8347 (m-40) REVERT: B 61 MET cc_start: 0.8795 (ppp) cc_final: 0.8581 (ppp) REVERT: B 76 ASP cc_start: 0.8005 (p0) cc_final: 0.7132 (t0) REVERT: B 254 ASP cc_start: 0.7652 (t0) cc_final: 0.7320 (t0) REVERT: B 289 TYR cc_start: 0.7513 (m-80) cc_final: 0.7307 (m-80) REVERT: B 308 LEU cc_start: 0.8911 (mt) cc_final: 0.8354 (mt) REVERT: B 322 ASP cc_start: 0.7348 (p0) cc_final: 0.6952 (p0) REVERT: B 337 LYS cc_start: 0.8947 (mptt) cc_final: 0.8435 (mptt) REVERT: G 20 LYS cc_start: 0.7975 (pptt) cc_final: 0.7441 (tptp) REVERT: N 18 LEU cc_start: 0.8368 (tp) cc_final: 0.8039 (tp) REVERT: N 20 LEU cc_start: 0.8483 (mt) cc_final: 0.8249 (mt) REVERT: N 77 ASN cc_start: 0.7843 (t0) cc_final: 0.7290 (t0) REVERT: N 83 MET cc_start: 0.8010 (mtm) cc_final: 0.7751 (mtm) REVERT: R 37 GLN cc_start: 0.9220 (mm-40) cc_final: 0.8803 (tm-30) REVERT: R 38 LYS cc_start: 0.9220 (pttm) cc_final: 0.8484 (pttm) REVERT: R 67 ASP cc_start: 0.8074 (p0) cc_final: 0.7537 (p0) REVERT: R 163 SER cc_start: 0.9278 (m) cc_final: 0.9029 (p) REVERT: R 179 ILE cc_start: 0.9276 (mm) cc_final: 0.8732 (mm) REVERT: R 184 PHE cc_start: 0.8293 (m-10) cc_final: 0.7952 (m-10) REVERT: R 230 PHE cc_start: 0.8380 (t80) cc_final: 0.7787 (t80) outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 0.2278 time to fit residues: 90.0786 Evaluate side-chains 222 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 0.6980 chunk 93 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 25 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- 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 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 171 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.6795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9037 Z= 0.263 Angle : 0.645 8.306 12252 Z= 0.342 Chirality : 0.043 0.138 1338 Planarity : 0.004 0.036 1556 Dihedral : 5.459 47.498 1220 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 20.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.26), residues: 1072 helix: 1.08 (0.26), residues: 394 sheet: -1.52 (0.37), residues: 192 loop : -1.56 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 297 HIS 0.011 0.002 HIS B 225 PHE 0.017 0.002 PHE R 315 TYR 0.017 0.002 TYR B 105 ARG 0.005 0.000 ARG R 170 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8061 (pm20) cc_final: 0.7826 (pp20) REVERT: A 270 LEU cc_start: 0.9069 (mt) cc_final: 0.8852 (mt) REVERT: A 272 LEU cc_start: 0.9396 (tp) cc_final: 0.9101 (tp) REVERT: A 279 ASN cc_start: 0.7645 (t0) cc_final: 0.7359 (t0) REVERT: A 386 MET cc_start: 0.7966 (tmm) cc_final: 0.7110 (tmm) REVERT: A 389 ARG cc_start: 0.7741 (ppt170) cc_final: 0.7333 (ppt170) REVERT: A 390 GLN cc_start: 0.8942 (mt0) cc_final: 0.8064 (mt0) REVERT: B 12 GLU cc_start: 0.8488 (pt0) cc_final: 0.8266 (pt0) REVERT: B 16 ASN cc_start: 0.8694 (m-40) cc_final: 0.8436 (m-40) REVERT: B 76 ASP cc_start: 0.8057 (p0) cc_final: 0.7644 (p0) REVERT: B 186 ASP cc_start: 0.6604 (m-30) cc_final: 0.6398 (m-30) REVERT: B 254 ASP cc_start: 0.7721 (t0) cc_final: 0.7405 (t0) REVERT: B 261 LEU cc_start: 0.9173 (mm) cc_final: 0.8955 (mm) REVERT: B 262 MET cc_start: 0.7978 (ttp) cc_final: 0.7683 (ptm) REVERT: B 308 LEU cc_start: 0.8892 (mt) cc_final: 0.8366 (mt) REVERT: B 322 ASP cc_start: 0.7548 (p0) cc_final: 0.7110 (p0) REVERT: N 18 LEU cc_start: 0.8402 (tp) cc_final: 0.8162 (tp) REVERT: N 20 LEU cc_start: 0.8479 (mt) cc_final: 0.8245 (mt) REVERT: N 50 ASP cc_start: 0.9318 (p0) cc_final: 0.8972 (p0) REVERT: N 77 ASN cc_start: 0.7774 (t0) cc_final: 0.7008 (t0) REVERT: N 83 MET cc_start: 0.8087 (mtm) cc_final: 0.7811 (mtm) REVERT: R 37 GLN cc_start: 0.9147 (mm-40) cc_final: 0.8631 (tm-30) REVERT: R 38 LYS cc_start: 0.9281 (pttm) cc_final: 0.8929 (pttm) REVERT: R 67 ASP cc_start: 0.8303 (p0) cc_final: 0.7275 (p0) REVERT: R 163 SER cc_start: 0.9233 (m) cc_final: 0.9028 (p) REVERT: R 179 ILE cc_start: 0.9309 (mm) cc_final: 0.8614 (mm) REVERT: R 184 PHE cc_start: 0.8318 (m-10) cc_final: 0.8002 (m-10) REVERT: R 190 ARG cc_start: 0.8434 (tpp80) cc_final: 0.8007 (tpt-90) REVERT: R 230 PHE cc_start: 0.8419 (t80) cc_final: 0.7938 (t80) REVERT: R 415 LYS cc_start: 0.9185 (ptpp) cc_final: 0.8808 (ptpp) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.1969 time to fit residues: 73.4301 Evaluate side-chains 216 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 9.9990 chunk 58 optimal weight: 20.0000 chunk 75 optimal weight: 0.0870 chunk 87 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 chunk 63 optimal weight: 0.9980 chunk 41 optimal weight: 8.9990 overall best weight: 2.1962 ------------------------------------------------------------------------------- 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 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.6915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9037 Z= 0.208 Angle : 0.632 8.762 12252 Z= 0.331 Chirality : 0.043 0.152 1338 Planarity : 0.004 0.078 1556 Dihedral : 5.420 43.925 1220 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.11 % Allowed : 1.48 % Favored : 98.42 % 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: -0.77 (0.26), residues: 1072 helix: 1.19 (0.26), residues: 401 sheet: -1.42 (0.38), residues: 180 loop : -1.60 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 284 HIS 0.016 0.002 HIS R 171 PHE 0.015 0.001 PHE A 273 TYR 0.017 0.002 TYR B 105 ARG 0.005 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 277 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 MET cc_start: 0.8708 (mmm) cc_final: 0.8504 (mmm) REVERT: A 270 LEU cc_start: 0.9057 (mt) cc_final: 0.8781 (mt) REVERT: A 386 MET cc_start: 0.8093 (tmm) cc_final: 0.7239 (tmm) REVERT: A 390 GLN cc_start: 0.9047 (mt0) cc_final: 0.8369 (mt0) REVERT: B 12 GLU cc_start: 0.8518 (pt0) cc_final: 0.8302 (pt0) REVERT: B 16 ASN cc_start: 0.8713 (m-40) cc_final: 0.8461 (m-40) REVERT: B 61 MET cc_start: 0.8802 (ppp) cc_final: 0.8595 (ppp) REVERT: B 76 ASP cc_start: 0.7882 (p0) cc_final: 0.6625 (t0) REVERT: B 121 CYS cc_start: 0.8409 (m) cc_final: 0.8205 (m) REVERT: B 254 ASP cc_start: 0.7674 (t0) cc_final: 0.7372 (t0) REVERT: B 308 LEU cc_start: 0.8788 (mt) cc_final: 0.8396 (mp) REVERT: B 322 ASP cc_start: 0.7617 (p0) cc_final: 0.7179 (p0) REVERT: G 20 LYS cc_start: 0.7943 (pptt) cc_final: 0.7314 (tptt) REVERT: N 18 LEU cc_start: 0.8093 (tp) cc_final: 0.7634 (tp) REVERT: N 20 LEU cc_start: 0.8468 (mt) cc_final: 0.8251 (mt) REVERT: N 50 ASP cc_start: 0.9316 (p0) cc_final: 0.8959 (p0) REVERT: N 77 ASN cc_start: 0.8114 (t0) cc_final: 0.7332 (t0) REVERT: N 83 MET cc_start: 0.8178 (mtm) cc_final: 0.7814 (mtm) REVERT: R 37 GLN cc_start: 0.9056 (mm-40) cc_final: 0.8637 (tm-30) REVERT: R 38 LYS cc_start: 0.9252 (pttm) cc_final: 0.8965 (pttm) REVERT: R 184 PHE cc_start: 0.8251 (m-10) cc_final: 0.8000 (m-10) REVERT: R 230 PHE cc_start: 0.8393 (t80) cc_final: 0.7973 (t80) REVERT: R 415 LYS cc_start: 0.9198 (ptpp) cc_final: 0.8845 (ptpp) outliers start: 1 outliers final: 0 residues processed: 278 average time/residue: 0.1986 time to fit residues: 76.2353 Evaluate side-chains 221 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN N 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.7253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9037 Z= 0.248 Angle : 0.652 8.941 12252 Z= 0.341 Chirality : 0.044 0.196 1338 Planarity : 0.004 0.029 1556 Dihedral : 5.649 46.515 1220 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 20.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.26), residues: 1072 helix: 1.21 (0.26), residues: 394 sheet: -1.38 (0.36), residues: 197 loop : -1.58 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP R 284 HIS 0.013 0.001 HIS B 225 PHE 0.016 0.002 PHE A 273 TYR 0.020 0.002 TYR N 95 ARG 0.007 0.001 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 LEU cc_start: 0.8933 (mt) cc_final: 0.8698 (mt) REVERT: A 358 TYR cc_start: 0.6406 (m-10) cc_final: 0.5982 (m-10) REVERT: A 386 MET cc_start: 0.8135 (tmm) cc_final: 0.7299 (tmm) REVERT: A 390 GLN cc_start: 0.9051 (mt0) cc_final: 0.8519 (mt0) REVERT: B 12 GLU cc_start: 0.8569 (pt0) cc_final: 0.8355 (pt0) REVERT: B 16 ASN cc_start: 0.8771 (m-40) cc_final: 0.8504 (m-40) REVERT: B 76 ASP cc_start: 0.7929 (p0) cc_final: 0.6747 (t0) REVERT: B 121 CYS cc_start: 0.8575 (m) cc_final: 0.8367 (m) REVERT: B 254 ASP cc_start: 0.7691 (t0) cc_final: 0.7435 (t0) REVERT: B 308 LEU cc_start: 0.8694 (mt) cc_final: 0.7765 (mp) REVERT: B 322 ASP cc_start: 0.7616 (p0) cc_final: 0.7330 (p0) REVERT: B 337 LYS cc_start: 0.8845 (mmtm) cc_final: 0.8624 (mmtt) REVERT: N 18 LEU cc_start: 0.8225 (tp) cc_final: 0.7767 (tp) REVERT: N 20 LEU cc_start: 0.8432 (mt) cc_final: 0.8142 (mt) REVERT: N 33 LYS cc_start: 0.8769 (pptt) cc_final: 0.8424 (ptpp) REVERT: N 50 ASP cc_start: 0.9377 (p0) cc_final: 0.9053 (p0) REVERT: N 77 ASN cc_start: 0.8112 (t0) cc_final: 0.7485 (t0) REVERT: N 83 MET cc_start: 0.8101 (mtm) cc_final: 0.7705 (mtm) REVERT: R 37 GLN cc_start: 0.9084 (mm-40) cc_final: 0.8747 (tm-30) REVERT: R 38 LYS cc_start: 0.9269 (pttm) cc_final: 0.8934 (pttt) REVERT: R 230 PHE cc_start: 0.8349 (t80) cc_final: 0.7801 (t80) REVERT: R 284 TRP cc_start: 0.7897 (t60) cc_final: 0.7643 (t60) REVERT: R 412 GLU cc_start: 0.8159 (mp0) cc_final: 0.7932 (mp0) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.1950 time to fit residues: 72.6149 Evaluate side-chains 209 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 75 optimal weight: 0.0970 chunk 29 optimal weight: 0.0040 chunk 86 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 63 optimal weight: 0.0010 chunk 101 optimal weight: 8.9990 overall best weight: 1.0200 ------------------------------------------------------------------------------- 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 278 ASN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN R 171 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.7192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9037 Z= 0.173 Angle : 0.636 8.998 12252 Z= 0.327 Chirality : 0.043 0.158 1338 Planarity : 0.003 0.027 1556 Dihedral : 5.193 38.837 1220 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % 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: -0.61 (0.26), residues: 1072 helix: 1.43 (0.26), residues: 387 sheet: -1.37 (0.36), residues: 193 loop : -1.51 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP R 284 HIS 0.010 0.001 HIS B 225 PHE 0.014 0.001 PHE B 278 TYR 0.017 0.001 TYR B 105 ARG 0.007 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 LEU cc_start: 0.8929 (mt) cc_final: 0.8714 (mt) REVERT: A 358 TYR cc_start: 0.6488 (m-10) cc_final: 0.6221 (m-10) REVERT: A 386 MET cc_start: 0.7982 (tmm) cc_final: 0.7472 (tmm) REVERT: A 390 GLN cc_start: 0.8827 (mt0) cc_final: 0.8341 (mt0) REVERT: B 12 GLU cc_start: 0.8549 (pt0) cc_final: 0.8343 (pt0) REVERT: B 16 ASN cc_start: 0.8723 (m-40) cc_final: 0.8457 (m-40) REVERT: B 76 ASP cc_start: 0.7853 (p0) cc_final: 0.6549 (t0) REVERT: B 121 CYS cc_start: 0.8546 (m) cc_final: 0.8345 (m) REVERT: B 254 ASP cc_start: 0.7556 (t0) cc_final: 0.7311 (t0) REVERT: B 308 LEU cc_start: 0.8597 (mt) cc_final: 0.7797 (mp) REVERT: B 322 ASP cc_start: 0.7554 (p0) cc_final: 0.7134 (p0) REVERT: G 20 LYS cc_start: 0.7950 (pptt) cc_final: 0.7270 (tptt) REVERT: N 18 LEU cc_start: 0.8167 (tp) cc_final: 0.7744 (tp) REVERT: N 20 LEU cc_start: 0.8420 (mt) cc_final: 0.8087 (mt) REVERT: N 50 ASP cc_start: 0.9307 (p0) cc_final: 0.8874 (p0) REVERT: N 77 ASN cc_start: 0.8067 (t0) cc_final: 0.7263 (t0) REVERT: N 81 LEU cc_start: 0.8596 (tp) cc_final: 0.8390 (tp) REVERT: N 83 MET cc_start: 0.8102 (mtm) cc_final: 0.7699 (mtm) REVERT: R 38 LYS cc_start: 0.9239 (pttm) cc_final: 0.8994 (pttm) REVERT: R 176 ARG cc_start: 0.8029 (pmt-80) cc_final: 0.7824 (pmt-80) REVERT: R 230 PHE cc_start: 0.8343 (t80) cc_final: 0.7924 (t80) REVERT: R 234 GLN cc_start: 0.7920 (tm-30) cc_final: 0.7652 (tm-30) REVERT: R 412 GLU cc_start: 0.8347 (mp0) cc_final: 0.7910 (mp0) REVERT: R 414 ARG cc_start: 0.7882 (mmt180) cc_final: 0.7262 (tpt170) outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.1991 time to fit residues: 79.5540 Evaluate side-chains 226 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 0.0770 chunk 48 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 106 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 overall best weight: 2.0142 ------------------------------------------------------------------------------- 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 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.7423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9037 Z= 0.208 Angle : 0.644 8.471 12252 Z= 0.337 Chirality : 0.044 0.164 1338 Planarity : 0.003 0.029 1556 Dihedral : 5.358 44.993 1220 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: -0.63 (0.26), residues: 1072 helix: 1.39 (0.27), residues: 388 sheet: -1.41 (0.37), residues: 191 loop : -1.48 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP R 284 HIS 0.012 0.002 HIS B 225 PHE 0.015 0.001 PHE B 278 TYR 0.014 0.002 TYR N 117 ARG 0.005 0.000 ARG A 389 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 ASP cc_start: 0.7233 (t0) cc_final: 0.6976 (t70) REVERT: A 346 LEU cc_start: 0.8932 (mt) cc_final: 0.8698 (mt) REVERT: A 358 TYR cc_start: 0.6791 (m-10) cc_final: 0.6227 (m-10) REVERT: A 386 MET cc_start: 0.8056 (tmm) cc_final: 0.7687 (tmm) REVERT: A 389 ARG cc_start: 0.7988 (ppt170) cc_final: 0.7755 (ppt170) REVERT: A 390 GLN cc_start: 0.8871 (mt0) cc_final: 0.8177 (mt0) REVERT: B 12 GLU cc_start: 0.8582 (pt0) cc_final: 0.8351 (pt0) REVERT: B 16 ASN cc_start: 0.8733 (m-40) cc_final: 0.8473 (m-40) REVERT: B 52 ARG cc_start: 0.7373 (mpp80) cc_final: 0.7151 (mpp80) REVERT: B 76 ASP cc_start: 0.7735 (p0) cc_final: 0.6422 (t0) REVERT: B 186 ASP cc_start: 0.6432 (m-30) cc_final: 0.6219 (m-30) REVERT: B 254 ASP cc_start: 0.7613 (t0) cc_final: 0.7311 (t0) REVERT: B 322 ASP cc_start: 0.7573 (p0) cc_final: 0.7076 (p0) REVERT: G 20 LYS cc_start: 0.7982 (pptt) cc_final: 0.7319 (tptt) REVERT: N 6 GLU cc_start: 0.6414 (pm20) cc_final: 0.6157 (pm20) REVERT: N 18 LEU cc_start: 0.8233 (tp) cc_final: 0.7814 (tp) REVERT: N 20 LEU cc_start: 0.8408 (mt) cc_final: 0.8141 (mt) REVERT: N 33 LYS cc_start: 0.8567 (pptt) cc_final: 0.8242 (ptpt) REVERT: N 50 ASP cc_start: 0.9328 (p0) cc_final: 0.8950 (p0) REVERT: N 77 ASN cc_start: 0.7992 (t0) cc_final: 0.7121 (t0) REVERT: N 83 MET cc_start: 0.8138 (mtm) cc_final: 0.7684 (mtm) REVERT: N 120 GLN cc_start: 0.6864 (pt0) cc_final: 0.6604 (pp30) REVERT: N 122 THR cc_start: 0.4360 (p) cc_final: 0.4125 (p) REVERT: R 48 ARG cc_start: 0.8705 (tmt-80) cc_final: 0.8405 (tpt90) REVERT: R 69 TYR cc_start: 0.8451 (t80) cc_final: 0.8217 (t80) REVERT: R 230 PHE cc_start: 0.8334 (t80) cc_final: 0.7905 (t80) REVERT: R 414 ARG cc_start: 0.7884 (mmt180) cc_final: 0.7315 (tpt170) REVERT: R 415 LYS cc_start: 0.9125 (ptpp) cc_final: 0.8871 (pttm) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.1947 time to fit residues: 72.0956 Evaluate side-chains 215 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 5.9990 chunk 78 optimal weight: 0.0670 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 85 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 74 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- 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 41 HIS ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 171 HIS R 374 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.111102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.092618 restraints weight = 31085.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.094883 restraints weight = 20757.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.096522 restraints weight = 15381.479| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.7429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9037 Z= 0.168 Angle : 0.622 7.251 12252 Z= 0.324 Chirality : 0.044 0.160 1338 Planarity : 0.003 0.028 1556 Dihedral : 4.988 34.229 1220 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: -0.61 (0.26), residues: 1072 helix: 1.28 (0.27), residues: 397 sheet: -1.29 (0.37), residues: 193 loop : -1.45 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP R 284 HIS 0.010 0.001 HIS B 225 PHE 0.014 0.001 PHE B 278 TYR 0.016 0.001 TYR N 117 ARG 0.004 0.000 ARG A 389 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2289.73 seconds wall clock time: 42 minutes 5.89 seconds (2525.89 seconds total)