Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 02:12:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c2e_30274/04_2023/7c2e_30274_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c2e_30274/04_2023/7c2e_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_30274/04_2023/7c2e_30274.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c2e_30274/04_2023/7c2e_30274.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c2e_30274/04_2023/7c2e_30274_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c2e_30274/04_2023/7c2e_30274_neut_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-1.21rc1-4938/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: 5.27, per 1000 atoms: 0.60 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: 3.50 Conformation dependent library (CDL) restraints added in 1.4 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: 0.71 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: 2.26 Time building geometry restraints manager: 3.82 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: 5073 15.00 - 30.00: 189 30.00 - 45.00: 59 45.00 - 60.00: 6 60.00 - 75.00: 3 Dihedral angle restraints: 5330 sinusoidal: 2140 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 5327 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: 1.190 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: 0.020 Extract box with map and model: 2.640 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 25.950 Find NCS groups from input model: 0.250 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:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.480 ------------------------------------------------------------------------------- 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 : 9.284 75.003 3248 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 % 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 *********************** 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 : 1.105 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 outliers start: 0 outliers final: 0 residues processed: 488 average time/residue: 0.2622 time to fit residues: 165.3963 Evaluate side-chains 255 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 1.137 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6687 ------------------------------------------------------------------------------- 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: 0.8980 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 32 optimal weight: 20.0000 chunk 50 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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** A 390 GLN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 9037 Z= 0.265 Angle : 0.663 12.608 12252 Z= 0.345 Chirality : 0.043 0.161 1338 Planarity : 0.005 0.040 1556 Dihedral : 5.320 48.177 1214 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer Outliers : 0.21 % 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: -1.89 (0.24), residues: 1072 helix: 0.47 (0.24), residues: 411 sheet: -2.43 (0.34), residues: 195 loop : -2.29 (0.26), residues: 466 *********************** 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 319 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 317 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: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 317 average time/residue: 0.2266 time to fit residues: 95.9435 Evaluate side-chains 224 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 223 time to evaluate : 1.103 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0803 time to fit residues: 1.6268 ------------------------------------------------------------------------------- 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: 20.0000 chunk 30 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 78 optimal weight: 0.0980 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 HIS R 171 HIS R 240 ASN R 304 ASN R 407 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.5434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 9037 Z= 0.184 Angle : 0.597 10.339 12252 Z= 0.308 Chirality : 0.042 0.141 1338 Planarity : 0.004 0.031 1556 Dihedral : 5.046 35.398 1214 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.25), residues: 1072 helix: 0.86 (0.26), residues: 412 sheet: -1.99 (0.37), residues: 182 loop : -2.05 (0.26), residues: 478 *********************** 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 296 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 296 time to evaluate : 1.107 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 outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.2127 time to fit residues: 87.0792 Evaluate side-chains 210 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 1.141 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5119 ------------------------------------------------------------------------------- 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: 6.9990 chunk 73 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 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 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN B 142 HIS B 340 ASN ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 171 HIS R 173 HIS R 240 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.6246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 9037 Z= 0.268 Angle : 0.648 7.677 12252 Z= 0.340 Chirality : 0.043 0.157 1338 Planarity : 0.004 0.040 1556 Dihedral : 5.396 43.770 1214 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 19.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.26), residues: 1072 helix: 1.03 (0.26), residues: 406 sheet: -1.86 (0.36), residues: 187 loop : -1.80 (0.27), residues: 479 *********************** 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 278 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 1.025 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 outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.2138 time to fit residues: 82.0395 Evaluate side-chains 214 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 1.116 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4996 ------------------------------------------------------------------------------- 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: 7.9990 chunk 58 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 chunk 0 optimal weight: 2.9990 chunk 52 optimal weight: 20.0000 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 74 ASN R 171 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.6463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 9037 Z= 0.214 Angle : 0.597 7.796 12252 Z= 0.312 Chirality : 0.042 0.152 1338 Planarity : 0.004 0.038 1556 Dihedral : 5.219 37.306 1214 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.26), residues: 1072 helix: 1.25 (0.27), residues: 400 sheet: -1.73 (0.36), residues: 188 loop : -1.80 (0.27), residues: 484 *********************** 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 274 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 1.052 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 outliers start: 0 outliers final: 0 residues processed: 274 average time/residue: 0.2221 time to fit residues: 82.5333 Evaluate side-chains 204 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.147 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4338 ------------------------------------------------------------------------------- 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: 10.0000 chunk 93 optimal weight: 0.6980 chunk 20 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 85 optimal weight: 4.9990 chunk 47 optimal weight: 0.4980 chunk 8 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 99 optimal weight: 0.8980 overall best weight: 2.2184 ------------------------------------------------------------------------------- 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 ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN N 39 GLN ** R 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.6703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 9037 Z= 0.203 Angle : 0.590 7.862 12252 Z= 0.311 Chirality : 0.042 0.146 1338 Planarity : 0.003 0.032 1556 Dihedral : 5.252 38.797 1214 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.26), residues: 1072 helix: 1.40 (0.26), residues: 392 sheet: -1.70 (0.37), residues: 183 loop : -1.73 (0.27), residues: 497 *********************** 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 267 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 1.144 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 outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.1981 time to fit residues: 74.0057 Evaluate side-chains 199 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 1.033 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3514 ------------------------------------------------------------------------------- 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: 1.9990 chunk 58 optimal weight: 30.0000 chunk 75 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 62 optimal weight: 20.0000 chunk 47 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 220 HIS ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN N 74 ASN ** R 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 407 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.7142 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= 0.280 Angle : 0.679 7.476 12252 Z= 0.355 Chirality : 0.044 0.159 1338 Planarity : 0.004 0.039 1556 Dihedral : 5.669 43.400 1214 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 22.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer Outliers : 0.11 % 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: -0.95 (0.26), residues: 1072 helix: 1.13 (0.26), residues: 394 sheet: -1.75 (0.37), residues: 186 loop : -1.64 (0.27), residues: 492 *********************** 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 268 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 267 time to evaluate : 1.169 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 outliers start: 1 outliers final: 0 residues processed: 267 average time/residue: 0.2165 time to fit residues: 80.9381 Evaluate side-chains 202 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 1.166 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6043 ------------------------------------------------------------------------------- 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: 10.0000 chunk 31 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 70 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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 390 GLN ** 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 74 ASN ** R 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.7300 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= 0.243 Angle : 0.654 7.296 12252 Z= 0.345 Chirality : 0.045 0.201 1338 Planarity : 0.004 0.033 1556 Dihedral : 5.615 41.535 1214 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 21.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.26), residues: 1072 helix: 1.16 (0.26), residues: 387 sheet: -1.78 (0.36), residues: 193 loop : -1.61 (0.27), residues: 492 *********************** 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 265 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.2047 time to fit residues: 75.2237 Evaluate side-chains 209 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.076 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4153 ------------------------------------------------------------------------------- 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: 0.0670 chunk 96 optimal weight: 0.3980 chunk 98 optimal weight: 2.9990 chunk 57 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 75 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 95 optimal weight: 0.0370 chunk 63 optimal weight: 7.9990 chunk 101 optimal weight: 0.9980 overall best weight: 0.4596 ------------------------------------------------------------------------------- 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 267 GLN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 74 ASN ** R 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.7236 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= 0.170 Angle : 0.655 7.534 12252 Z= 0.339 Chirality : 0.044 0.223 1338 Planarity : 0.003 0.033 1556 Dihedral : 5.179 29.597 1214 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.26), residues: 1072 helix: 1.37 (0.27), residues: 388 sheet: -1.63 (0.36), residues: 191 loop : -1.52 (0.27), residues: 493 *********************** 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 273 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 1.102 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 outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.2158 time to fit residues: 82.3443 Evaluate side-chains 202 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 1.151 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5149 ------------------------------------------------------------------------------- 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: 20.0000 chunk 48 optimal weight: 0.2980 chunk 70 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- 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 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.7428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 9037 Z= 0.208 Angle : 0.667 7.291 12252 Z= 0.356 Chirality : 0.044 0.188 1338 Planarity : 0.003 0.033 1556 Dihedral : 5.321 39.995 1214 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.26), residues: 1072 helix: 1.12 (0.27), residues: 396 sheet: -1.62 (0.36), residues: 195 loop : -1.52 (0.27), residues: 481 ********************** 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 262 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 1.147 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 outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.1890 time to fit residues: 69.9732 Evaluate side-chains 200 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.198 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4678 ------------------------------------------------------------------------------- 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: 0.9990 chunk 78 optimal weight: 0.0070 chunk 12 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.0170 chunk 74 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 overall best weight: 1.2042 ------------------------------------------------------------------------------- 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 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN ** R 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.111130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.093035 restraints weight = 31292.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.095383 restraints weight = 20754.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.097047 restraints weight = 15176.412| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.7456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 9037 Z= 0.176 Angle : 0.654 7.397 12252 Z= 0.345 Chirality : 0.044 0.173 1338 Planarity : 0.003 0.043 1556 Dihedral : 5.118 36.772 1214 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.26), residues: 1072 helix: 1.16 (0.27), residues: 393 sheet: -1.49 (0.37), residues: 188 loop : -1.51 (0.27), residues: 491 =============================================================================== Job complete usr+sys time: 2293.34 seconds wall clock time: 42 minutes 19.98 seconds (2539.98 seconds total)