Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:48:33 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl9_25195/11_2022/7sl9_25195_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl9_25195/11_2022/7sl9_25195.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl9_25195/11_2022/7sl9_25195.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl9_25195/11_2022/7sl9_25195.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl9_25195/11_2022/7sl9_25195_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sl9_25195/11_2022/7sl9_25195_neut_updated.pdb" } resolution = 3.5 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= 0.007 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 80": "NH1" <-> "NH2" Residue "A ARG 122": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A GLU 366": "OE1" <-> "OE2" Residue "B ARG 33": "NH1" <-> "NH2" Residue "B GLU 90": "OE1" <-> "OE2" Residue "B ARG 107": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 4712 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3763 Classifications: {'peptide': 497} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 19, 'TRANS': 477} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 943 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'BUA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.19, per 1000 atoms: 0.68 Number of scatterers: 4712 At special positions: 0 Unit cell: (91.16, 77.38, 90.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 844 8.00 N 749 7.00 C 3091 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 480 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 97 " distance=2.03 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: 2.05 Conformation dependent library (CDL) restraints added in 740.5 milliseconds 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1120 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 2 sheets defined 55.9% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 15 through 33 removed outlier: 3.795A pdb=" N SER A 25 " --> pdb=" O MET A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 65 removed outlier: 3.549A pdb=" N LEU A 59 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 72 No H-bonds generated for 'chain 'A' and resid 69 through 72' Processing helix chain 'A' and resid 74 through 101 removed outlier: 3.815A pdb=" N ARG A 80 " --> pdb=" O SER A 76 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ALA A 83 " --> pdb=" O TYR A 79 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N ILE A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N PHE A 85 " --> pdb=" O PHE A 81 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N SER A 86 " --> pdb=" O GLY A 82 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ILE A 87 " --> pdb=" O ALA A 83 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N PHE A 88 " --> pdb=" O ILE A 84 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ALA A 89 " --> pdb=" O PHE A 85 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N PHE A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR A 91 " --> pdb=" O ILE A 87 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A 96 " --> pdb=" O TYR A 92 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE A 98 " --> pdb=" O PHE A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 119 through 122 No H-bonds generated for 'chain 'A' and resid 119 through 122' Processing helix chain 'A' and resid 126 through 129 No H-bonds generated for 'chain 'A' and resid 126 through 129' Processing helix chain 'A' and resid 132 through 158 removed outlier: 3.689A pdb=" N GLY A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ILE A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Proline residue: A 150 - end of helix removed outlier: 4.035A pdb=" N GLN A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 174 removed outlier: 3.756A pdb=" N VAL A 172 " --> pdb=" O ALA A 168 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N CYS A 173 " --> pdb=" O THR A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 211 removed outlier: 3.991A pdb=" N PHE A 191 " --> pdb=" O TRP A 187 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLN A 192 " --> pdb=" O THR A 188 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 193 " --> pdb=" O ASP A 189 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA A 198 " --> pdb=" O GLY A 194 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 201 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 203 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN A 206 " --> pdb=" O SER A 202 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA A 207 " --> pdb=" O VAL A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 223 removed outlier: 4.029A pdb=" N ASN A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 257 removed outlier: 3.511A pdb=" N PHE A 251 " --> pdb=" O ILE A 247 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER A 255 " --> pdb=" O PHE A 251 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE A 256 " --> pdb=" O THR A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 268 removed outlier: 4.691A pdb=" N ARG A 266 " --> pdb=" O SER A 262 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N TYR A 267 " --> pdb=" O GLN A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 304 removed outlier: 3.652A pdb=" N LEU A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN A 283 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL A 285 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A 286 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N CYS A 297 " --> pdb=" O CYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 323 through 330 removed outlier: 3.622A pdb=" N LEU A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 368 removed outlier: 3.668A pdb=" N VAL A 342 " --> pdb=" O PRO A 338 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY A 348 " --> pdb=" O CYS A 344 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N THR A 349 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU A 350 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER A 351 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR A 364 " --> pdb=" O LEU A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 404 removed outlier: 3.730A pdb=" N GLN A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER A 389 " --> pdb=" O SER A 385 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL A 390 " --> pdb=" O GLN A 386 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER A 404 " --> pdb=" O ALA A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 418 removed outlier: 3.531A pdb=" N VAL A 416 " --> pdb=" O ALA A 412 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 432 removed outlier: 3.503A pdb=" N LEU A 427 " --> pdb=" O PRO A 423 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 462 removed outlier: 3.787A pdb=" N VAL A 444 " --> pdb=" O ILE A 440 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN A 461 " --> pdb=" O GLY A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 470 No H-bonds generated for 'chain 'A' and resid 467 through 470' Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 526 through 532 removed outlier: 4.139A pdb=" N VAL A 531 " --> pdb=" O VAL A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 542 removed outlier: 3.690A pdb=" N SER A 540 " --> pdb=" O GLY A 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 65 No H-bonds generated for 'chain 'B' and resid 63 through 65' Processing sheet with id= A, first strand: chain 'B' and resid 19 through 24 removed outlier: 3.775A pdb=" N THR B 79 " --> pdb=" O ASP B 74 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 39 through 41 removed outlier: 3.741A pdb=" N ALA B 93 " --> pdb=" O VAL B 120 " (cutoff:3.500A) 192 hydrogen bonds defined for protein. 567 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: 1.17 Time building geometry restraints manager: 2.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1428 1.34 - 1.46: 1175 1.46 - 1.58: 2183 1.58 - 1.70: 0 1.70 - 1.81: 43 Bond restraints: 4829 Sorted by residual: bond pdb=" C THR A 510 " pdb=" N PRO A 511 " ideal model delta sigma weight residual 1.336 1.358 -0.023 1.08e-02 8.57e+03 4.38e+00 bond pdb=" C SER A 317 " pdb=" N ALA A 318 " ideal model delta sigma weight residual 1.329 1.276 0.052 3.03e-02 1.09e+03 2.99e+00 bond pdb=" C3 BUA A 701 " pdb=" C4 BUA A 701 " ideal model delta sigma weight residual 1.539 1.506 0.033 2.00e-02 2.50e+03 2.69e+00 bond pdb=" N LYS A 314 " pdb=" CA LYS A 314 " ideal model delta sigma weight residual 1.460 1.485 -0.024 1.51e-02 4.39e+03 2.58e+00 bond pdb=" N VAL A 316 " pdb=" CA VAL A 316 " ideal model delta sigma weight residual 1.458 1.440 0.018 1.19e-02 7.06e+03 2.39e+00 ... (remaining 4824 not shown) Histogram of bond angle deviations from ideal: 98.81 - 105.85: 101 105.85 - 112.88: 2461 112.88 - 119.92: 1790 119.92 - 126.95: 2175 126.95 - 133.98: 65 Bond angle restraints: 6592 Sorted by residual: angle pdb=" N LYS A 315 " pdb=" CA LYS A 315 " pdb=" C LYS A 315 " ideal model delta sigma weight residual 110.35 122.13 -11.78 1.36e+00 5.41e-01 7.50e+01 angle pdb=" N VAL A 316 " pdb=" CA VAL A 316 " pdb=" C VAL A 316 " ideal model delta sigma weight residual 108.12 98.81 9.31 1.44e+00 4.82e-01 4.18e+01 angle pdb=" N GLN A 508 " pdb=" CA GLN A 508 " pdb=" C GLN A 508 " ideal model delta sigma weight residual 112.68 107.28 5.40 1.33e+00 5.65e-01 1.65e+01 angle pdb=" C PHE A 160 " pdb=" N ASP A 161 " pdb=" CA ASP A 161 " ideal model delta sigma weight residual 121.54 129.16 -7.62 1.91e+00 2.74e-01 1.59e+01 angle pdb=" C THR A 178 " pdb=" N LEU A 179 " pdb=" CA LEU A 179 " ideal model delta sigma weight residual 124.31 130.91 -6.60 1.67e+00 3.59e-01 1.56e+01 ... (remaining 6587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 2473 17.66 - 35.32: 236 35.32 - 52.98: 36 52.98 - 70.64: 7 70.64 - 88.30: 2 Dihedral angle restraints: 2754 sinusoidal: 983 harmonic: 1771 Sorted by residual: dihedral pdb=" CA TYR B 111 " pdb=" C TYR B 111 " pdb=" N TYR B 112 " pdb=" CA TYR B 112 " ideal model delta harmonic sigma weight residual -180.00 -150.42 -29.58 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA LEU A 409 " pdb=" C LEU A 409 " pdb=" N LEU A 410 " pdb=" CA LEU A 410 " ideal model delta harmonic sigma weight residual 180.00 157.76 22.24 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA ILE A 477 " pdb=" C ILE A 477 " pdb=" N GLN A 478 " pdb=" CA GLN A 478 " ideal model delta harmonic sigma weight residual -180.00 -157.94 -22.06 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 2751 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 695 0.092 - 0.184: 67 0.184 - 0.276: 6 0.276 - 0.368: 0 0.368 - 0.460: 1 Chirality restraints: 769 Sorted by residual: chirality pdb=" CA LYS A 315 " pdb=" N LYS A 315 " pdb=" C LYS A 315 " pdb=" CB LYS A 315 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.29e+00 chirality pdb=" CA VAL A 316 " pdb=" N VAL A 316 " pdb=" C VAL A 316 " pdb=" CB VAL A 316 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB VAL A 203 " pdb=" CA VAL A 203 " pdb=" CG1 VAL A 203 " pdb=" CG2 VAL A 203 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 766 not shown) Planarity restraints: 813 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 BUA A 701 " -0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C4 BUA A 701 " 0.067 2.00e-02 2.50e+03 pdb=" O1 BUA A 701 " -0.024 2.00e-02 2.50e+03 pdb=" O2 BUA A 701 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 309 " -0.040 5.00e-02 4.00e+02 6.06e-02 5.87e+00 pdb=" N PRO A 310 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 310 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 310 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 422 " 0.038 5.00e-02 4.00e+02 5.74e-02 5.27e+00 pdb=" N PRO A 423 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 423 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 423 " 0.032 5.00e-02 4.00e+02 ... (remaining 810 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1300 2.79 - 3.32: 4374 3.32 - 3.84: 7733 3.84 - 4.37: 9210 4.37 - 4.90: 15380 Nonbonded interactions: 37997 Sorted by model distance: nonbonded pdb=" O PRO A 472 " pdb=" OH TYR B 111 " model vdw 2.259 2.440 nonbonded pdb=" OG1 THR B 92 " pdb=" O VAL B 120 " model vdw 2.290 2.440 nonbonded pdb=" O GLY A 224 " pdb=" OG SER B 31 " model vdw 2.304 2.440 nonbonded pdb=" O ILE A 246 " pdb=" OG1 THR A 250 " model vdw 2.304 2.440 nonbonded pdb=" O THR A 250 " pdb=" OG1 THR A 254 " model vdw 2.312 2.440 ... (remaining 37992 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 3091 2.51 5 N 749 2.21 5 O 844 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.460 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: 2.160 Check model and map are aligned: 0.070 Convert atoms to be neutral: 0.050 Process input model: 17.330 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 23.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 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 : 0.005 0.060 4829 Z= 0.311 Angle : 0.951 11.781 6592 Z= 0.523 Chirality : 0.058 0.460 769 Planarity : 0.007 0.061 813 Dihedral : 13.950 88.296 1628 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer Outliers : 0.40 % 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: -6.01 (0.22), residues: 611 helix: -4.33 (0.11), residues: 357 sheet: -2.43 (0.71), residues: 45 loop : -3.26 (0.35), residues: 209 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 161 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 163 average time/residue: 0.1465 time to fit residues: 30.8948 Evaluate side-chains 126 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 0.538 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0454 time to fit residues: 0.7877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 6.9990 chunk 46 optimal weight: 0.0000 chunk 25 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN A 156 GLN A 358 ASN A 386 GLN B 3 GLN B 5 GLN ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 4829 Z= 0.216 Angle : 0.695 11.942 6592 Z= 0.352 Chirality : 0.043 0.191 769 Planarity : 0.005 0.042 813 Dihedral : 5.611 26.577 671 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer Outliers : 4.45 % 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: -3.95 (0.28), residues: 611 helix: -2.35 (0.21), residues: 355 sheet: -3.23 (0.67), residues: 47 loop : -2.62 (0.39), residues: 209 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 144 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 15 residues processed: 153 average time/residue: 0.1452 time to fit residues: 28.8917 Evaluate side-chains 136 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 0.452 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0519 time to fit residues: 2.1207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 ASN ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 4829 Z= 0.267 Angle : 0.703 11.427 6592 Z= 0.352 Chirality : 0.043 0.180 769 Planarity : 0.004 0.038 813 Dihedral : 5.407 26.185 671 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer Outliers : 4.25 % 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: -2.89 (0.31), residues: 611 helix: -1.33 (0.25), residues: 363 sheet: -3.23 (0.64), residues: 47 loop : -2.40 (0.41), residues: 201 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 141 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 14 residues processed: 154 average time/residue: 0.1420 time to fit residues: 28.3479 Evaluate side-chains 142 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 128 time to evaluate : 0.478 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0524 time to fit residues: 1.8563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 29 optimal weight: 0.0970 chunk 52 optimal weight: 2.9990 chunk 15 optimal weight: 0.0570 chunk 49 optimal weight: 1.9990 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN B 3 GLN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 4829 Z= 0.175 Angle : 0.663 9.135 6592 Z= 0.329 Chirality : 0.041 0.138 769 Planarity : 0.004 0.037 813 Dihedral : 5.084 23.046 671 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer Outliers : 2.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.32), residues: 611 helix: -0.77 (0.26), residues: 362 sheet: -3.23 (0.62), residues: 47 loop : -2.29 (0.41), residues: 202 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 142 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 148 average time/residue: 0.1456 time to fit residues: 28.1911 Evaluate side-chains 147 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 136 time to evaluate : 0.534 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0502 time to fit residues: 1.6538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 50 optimal weight: 30.0000 chunk 40 optimal weight: 2.9990 chunk 30 optimal weight: 0.0070 chunk 52 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 53 optimal weight: 20.0000 overall best weight: 0.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 ASN A 461 GLN ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN B 5 GLN ** B 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 4829 Z= 0.219 Angle : 0.686 10.658 6592 Z= 0.337 Chirality : 0.043 0.129 769 Planarity : 0.004 0.037 813 Dihedral : 5.112 23.566 671 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer Outliers : 1.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.34), residues: 611 helix: -0.48 (0.27), residues: 368 sheet: -3.04 (0.63), residues: 47 loop : -2.07 (0.44), residues: 196 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 137 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 138 average time/residue: 0.1492 time to fit residues: 26.8773 Evaluate side-chains 133 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 130 time to evaluate : 0.564 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0512 time to fit residues: 0.9823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.6980 chunk 34 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN B 5 GLN B 29 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 4829 Z= 0.204 Angle : 0.668 10.032 6592 Z= 0.332 Chirality : 0.042 0.139 769 Planarity : 0.004 0.036 813 Dihedral : 5.005 22.668 671 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.34), residues: 611 helix: -0.23 (0.28), residues: 361 sheet: -2.52 (0.72), residues: 47 loop : -2.11 (0.43), residues: 203 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 140 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 143 average time/residue: 0.1452 time to fit residues: 27.1945 Evaluate side-chains 136 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 130 time to evaluate : 0.542 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0547 time to fit residues: 1.2721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 0.0970 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN B 5 GLN B 78 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 4829 Z= 0.195 Angle : 0.666 9.500 6592 Z= 0.332 Chirality : 0.042 0.136 769 Planarity : 0.004 0.037 813 Dihedral : 4.874 21.813 671 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer Outliers : 1.01 % 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: -1.54 (0.34), residues: 611 helix: -0.23 (0.27), residues: 367 sheet: -2.46 (0.72), residues: 47 loop : -2.00 (0.44), residues: 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 137 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 139 average time/residue: 0.1417 time to fit residues: 26.0180 Evaluate side-chains 129 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 127 time to evaluate : 0.504 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0613 time to fit residues: 0.8932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN B 5 GLN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 4829 Z= 0.201 Angle : 0.679 8.858 6592 Z= 0.337 Chirality : 0.042 0.149 769 Planarity : 0.004 0.037 813 Dihedral : 4.856 22.000 671 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer Outliers : 1.82 % 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: -1.42 (0.34), residues: 611 helix: -0.12 (0.28), residues: 367 sheet: -2.47 (0.70), residues: 47 loop : -1.97 (0.44), residues: 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 132 time to evaluate : 0.562 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 136 average time/residue: 0.1488 time to fit residues: 26.5325 Evaluate side-chains 134 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 129 time to evaluate : 0.530 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0504 time to fit residues: 1.1175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 16 optimal weight: 0.0870 chunk 49 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 57 optimal weight: 0.0980 chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 4829 Z= 0.184 Angle : 0.687 9.301 6592 Z= 0.341 Chirality : 0.042 0.147 769 Planarity : 0.003 0.036 813 Dihedral : 4.810 20.913 671 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer Outliers : 0.61 % 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: -1.31 (0.34), residues: 611 helix: 0.02 (0.28), residues: 364 sheet: -2.30 (0.61), residues: 59 loop : -1.96 (0.46), residues: 188 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 133 time to evaluate : 0.559 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 134 average time/residue: 0.1502 time to fit residues: 26.5772 Evaluate side-chains 125 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 123 time to evaluate : 0.511 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0647 time to fit residues: 0.9572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 38 optimal weight: 0.2980 chunk 51 optimal weight: 0.3980 chunk 14 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 4829 Z= 0.226 Angle : 0.741 9.072 6592 Z= 0.368 Chirality : 0.043 0.147 769 Planarity : 0.003 0.037 813 Dihedral : 4.881 21.431 671 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer Outliers : 0.20 % 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: -1.27 (0.35), residues: 611 helix: 0.08 (0.28), residues: 369 sheet: -2.30 (0.61), residues: 59 loop : -2.05 (0.47), residues: 183 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1222 Ramachandran restraints generated. 611 Oldfield, 0 Emsley, 611 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 123 average time/residue: 0.1572 time to fit residues: 25.4531 Evaluate side-chains 121 residues out of total 504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 0.548 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0521 time to fit residues: 0.8281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 0.7980 chunk 20 optimal weight: 0.0170 chunk 49 optimal weight: 7.9990 chunk 6 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 41 optimal weight: 0.0070 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 ASN A 474 HIS ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.153215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.113847 restraints weight = 7701.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.117838 restraints weight = 4047.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.120360 restraints weight = 2794.020| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 4829 Z= 0.187 Angle : 0.722 9.247 6592 Z= 0.355 Chirality : 0.042 0.142 769 Planarity : 0.003 0.037 813 Dihedral : 4.820 20.474 671 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer Outliers : 0.61 % 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: -1.21 (0.35), residues: 611 helix: 0.10 (0.28), residues: 370 sheet: -2.21 (0.59), residues: 64 loop : -1.98 (0.48), residues: 177 =============================================================================== Job complete usr+sys time: 1304.53 seconds wall clock time: 24 minutes 20.62 seconds (1460.62 seconds total)