Starting phenix.real_space_refine on Sat Apr 6 21:41:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf5_34713/04_2024/8hf5_34713_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf5_34713/04_2024/8hf5_34713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf5_34713/04_2024/8hf5_34713.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf5_34713/04_2024/8hf5_34713.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf5_34713/04_2024/8hf5_34713_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf5_34713/04_2024/8hf5_34713_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 64 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 30 5.16 5 C 5732 2.51 5 N 1462 2.21 5 O 1686 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 277": "OD1" <-> "OD2" Residue "A ASP 335": "OD1" <-> "OD2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 371": "OD1" <-> "OD2" Residue "B TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8918 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4427 Classifications: {'peptide': 563} Link IDs: {'PTRANS': 12, 'TRANS': 550} Chain: "B" Number of atoms: 4427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4427 Classifications: {'peptide': 563} Link IDs: {'PTRANS': 12, 'TRANS': 550} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.80, per 1000 atoms: 0.54 Number of scatterers: 8918 At special positions: 0 Unit cell: (81.51, 80.652, 143.286, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 30 16.00 P 6 15.00 Mg 2 11.99 O 1686 8.00 N 1462 7.00 C 5732 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.42 Conformation dependent library (CDL) restraints added in 1.9 seconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2124 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 5 sheets defined 60.4% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 169 through 194 removed outlier: 3.561A pdb=" N LEU A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER A 191 " --> pdb=" O TYR A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 251 removed outlier: 4.391A pdb=" N LEU A 243 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER A 244 " --> pdb=" O ASP A 240 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR A 245 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N HIS A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 288 removed outlier: 4.085A pdb=" N ARG A 268 " --> pdb=" O GLU A 264 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE A 269 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 272 " --> pdb=" O ARG A 268 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASN A 273 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N SER A 274 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ILE A 275 " --> pdb=" O ASP A 271 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER A 281 " --> pdb=" O ASP A 277 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE A 286 " --> pdb=" O THR A 282 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE A 287 " --> pdb=" O ILE A 283 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 288 " --> pdb=" O LEU A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 301 removed outlier: 3.876A pdb=" N ILE A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 323 removed outlier: 4.932A pdb=" N LEU A 313 " --> pdb=" O PHE A 309 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ALA A 314 " --> pdb=" O MET A 310 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N LEU A 315 " --> pdb=" O THR A 311 " (cutoff:3.500A) Proline residue: A 316 - end of helix removed outlier: 4.110A pdb=" N VAL A 320 " --> pdb=" O PRO A 316 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE A 321 " --> pdb=" O ILE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 351 removed outlier: 3.690A pdb=" N MET A 332 " --> pdb=" O PRO A 328 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN A 333 " --> pdb=" O PHE A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 360 Processing helix chain 'A' and resid 363 through 416 removed outlier: 3.987A pdb=" N TYR A 384 " --> pdb=" O LYS A 380 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 387 " --> pdb=" O THR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 463 removed outlier: 3.870A pdb=" N VAL A 432 " --> pdb=" O ASN A 428 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TYR A 433 " --> pdb=" O THR A 429 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) Proline residue: A 437 - end of helix removed outlier: 4.467A pdb=" N LEU A 444 " --> pdb=" O ASN A 440 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N GLN A 445 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N THR A 446 " --> pdb=" O ILE A 442 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N LYS A 447 " --> pdb=" O ASN A 443 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLU A 460 " --> pdb=" O ASN A 456 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N VAL A 461 " --> pdb=" O ARG A 457 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TYR A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 530 Processing helix chain 'A' and resid 554 through 559 Processing helix chain 'A' and resid 574 through 578 Processing helix chain 'A' and resid 589 through 597 Processing helix chain 'A' and resid 624 through 637 Processing helix chain 'A' and resid 654 through 665 Processing helix chain 'A' and resid 679 through 682 No H-bonds generated for 'chain 'A' and resid 679 through 682' Processing helix chain 'A' and resid 701 through 705 Processing helix chain 'A' and resid 710 through 716 Processing helix chain 'B' and resid 158 through 161 No H-bonds generated for 'chain 'B' and resid 158 through 161' Processing helix chain 'B' and resid 166 through 195 removed outlier: 4.662A pdb=" N ASN B 170 " --> pdb=" O GLY B 166 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 251 removed outlier: 4.129A pdb=" N MET B 201 " --> pdb=" O PRO B 198 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ARG B 202 " --> pdb=" O ASP B 199 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B 205 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER B 209 " --> pdb=" O GLY B 206 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE B 239 " --> pdb=" O ARG B 236 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP B 240 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE B 242 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N LEU B 243 " --> pdb=" O ASP B 240 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE B 250 " --> pdb=" O LYS B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 273 Processing helix chain 'B' and resid 276 through 303 removed outlier: 3.722A pdb=" N LEU B 279 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA B 280 " --> pdb=" O ASP B 277 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 283 " --> pdb=" O ALA B 280 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 284 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 286 " --> pdb=" O ILE B 283 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE B 287 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 288 " --> pdb=" O SER B 285 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N VAL B 290 " --> pdb=" O PHE B 287 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N SER B 291 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B 296 " --> pdb=" O VAL B 293 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 300 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 311 Processing helix chain 'B' and resid 314 through 324 removed outlier: 4.096A pdb=" N VAL B 320 " --> pdb=" O PRO B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 352 Processing helix chain 'B' and resid 354 through 359 Processing helix chain 'B' and resid 365 through 386 removed outlier: 3.970A pdb=" N TYR B 384 " --> pdb=" O LYS B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 415 Processing helix chain 'B' and resid 421 through 462 removed outlier: 4.323A pdb=" N VAL B 432 " --> pdb=" O ASN B 428 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N TYR B 433 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE B 434 " --> pdb=" O LEU B 430 " (cutoff:3.500A) Proline residue: B 437 - end of helix removed outlier: 4.742A pdb=" N LEU B 444 " --> pdb=" O ASN B 440 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N GLN B 445 " --> pdb=" O ILE B 441 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N THR B 446 " --> pdb=" O ILE B 442 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N LYS B 447 " --> pdb=" O ASN B 443 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL B 453 " --> pdb=" O GLN B 449 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL B 461 " --> pdb=" O ARG B 457 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 Processing helix chain 'B' and resid 553 through 559 Processing helix chain 'B' and resid 574 through 578 Processing helix chain 'B' and resid 588 through 597 Processing helix chain 'B' and resid 601 through 604 No H-bonds generated for 'chain 'B' and resid 601 through 604' Processing helix chain 'B' and resid 624 through 637 Processing helix chain 'B' and resid 654 through 665 removed outlier: 3.595A pdb=" N ILE B 665 " --> pdb=" O VAL B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 682 removed outlier: 3.545A pdb=" N GLU B 682 " --> pdb=" O THR B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 707 Processing helix chain 'B' and resid 710 through 716 Processing sheet with id= A, first strand: chain 'A' and resid 485 through 487 Processing sheet with id= B, first strand: chain 'A' and resid 686 through 690 removed outlier: 6.833A pdb=" N LEU A 671 " --> pdb=" O VAL A 513 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N PHE A 515 " --> pdb=" O LEU A 671 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N PHE A 673 " --> pdb=" O PHE A 515 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N GLY A 517 " --> pdb=" O PHE A 673 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP A 646 " --> pdb=" O LEU A 563 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 489 through 491 removed outlier: 3.817A pdb=" N VAL A 489 " --> pdb=" O ILE A 503 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 503 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N TYR A 491 " --> pdb=" O SER A 501 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N SER A 501 " --> pdb=" O TYR A 491 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 540 through 542 removed outlier: 3.631A pdb=" N LEU B 505 " --> pdb=" O PHE B 486 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ILE B 503 " --> pdb=" O GLN B 488 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 695 through 699 removed outlier: 6.972A pdb=" N VAL B 689 " --> pdb=" O VAL B 696 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLU B 698 " --> pdb=" O VAL B 687 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL B 687 " --> pdb=" O GLU B 698 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU B 671 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N PHE B 515 " --> pdb=" O LEU B 671 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N PHE B 673 " --> pdb=" O PHE B 515 " (cutoff:3.500A) 467 hydrogen bonds defined for protein. 1212 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: 2.35 Time building geometry restraints manager: 3.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 1952 1.33 - 1.47: 2924 1.47 - 1.61: 4116 1.61 - 1.76: 0 1.76 - 1.90: 58 Bond restraints: 9050 Sorted by residual: bond pdb=" CA GLN A 226 " pdb=" C GLN A 226 " ideal model delta sigma weight residual 1.523 1.451 0.072 1.30e-02 5.92e+03 3.08e+01 bond pdb=" CA LEU B 645 " pdb=" C LEU B 645 " ideal model delta sigma weight residual 1.524 1.461 0.063 1.23e-02 6.61e+03 2.61e+01 bond pdb=" CA GLN A 612 " pdb=" C GLN A 612 " ideal model delta sigma weight residual 1.523 1.456 0.067 1.34e-02 5.57e+03 2.50e+01 bond pdb=" CA LEU A 222 " pdb=" C LEU A 222 " ideal model delta sigma weight residual 1.523 1.459 0.064 1.30e-02 5.92e+03 2.43e+01 bond pdb=" CA GLN A 235 " pdb=" C GLN A 235 " ideal model delta sigma weight residual 1.523 1.459 0.064 1.30e-02 5.92e+03 2.43e+01 ... (remaining 9045 not shown) Histogram of bond angle deviations from ideal: 96.94 - 104.53: 120 104.53 - 112.12: 4246 112.12 - 119.71: 3877 119.71 - 127.30: 3981 127.30 - 134.88: 54 Bond angle restraints: 12278 Sorted by residual: angle pdb=" N ARG A 202 " pdb=" CA ARG A 202 " pdb=" C ARG A 202 " ideal model delta sigma weight residual 113.28 99.73 13.55 1.22e+00 6.72e-01 1.23e+02 angle pdb=" N ALA B 169 " pdb=" CA ALA B 169 " pdb=" C ALA B 169 " ideal model delta sigma weight residual 111.28 121.97 -10.69 1.09e+00 8.42e-01 9.61e+01 angle pdb=" N PRO A 608 " pdb=" CA PRO A 608 " pdb=" C PRO A 608 " ideal model delta sigma weight residual 114.18 100.76 13.42 1.39e+00 5.18e-01 9.32e+01 angle pdb=" N TYR A 196 " pdb=" CA TYR A 196 " pdb=" C TYR A 196 " ideal model delta sigma weight residual 112.58 124.06 -11.48 1.22e+00 6.72e-01 8.86e+01 angle pdb=" N LYS B 163 " pdb=" CA LYS B 163 " pdb=" C LYS B 163 " ideal model delta sigma weight residual 114.12 101.16 12.96 1.39e+00 5.18e-01 8.69e+01 ... (remaining 12273 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.53: 5094 22.53 - 45.05: 343 45.05 - 67.58: 45 67.58 - 90.11: 6 90.11 - 112.63: 2 Dihedral angle restraints: 5490 sinusoidal: 2196 harmonic: 3294 Sorted by residual: dihedral pdb=" CA GLU A 469 " pdb=" C GLU A 469 " pdb=" N GLU A 470 " pdb=" CA GLU A 470 " ideal model delta harmonic sigma weight residual 180.00 151.59 28.41 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" C TYR A 216 " pdb=" N TYR A 216 " pdb=" CA TYR A 216 " pdb=" CB TYR A 216 " ideal model delta harmonic sigma weight residual -122.60 -135.72 13.12 0 2.50e+00 1.60e-01 2.76e+01 dihedral pdb=" C GLN A 200 " pdb=" N GLN A 200 " pdb=" CA GLN A 200 " pdb=" CB GLN A 200 " ideal model delta harmonic sigma weight residual -122.60 -135.31 12.71 0 2.50e+00 1.60e-01 2.58e+01 ... (remaining 5487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.142: 1355 0.142 - 0.285: 108 0.285 - 0.427: 26 0.427 - 0.569: 9 0.569 - 0.711: 4 Chirality restraints: 1502 Sorted by residual: chirality pdb=" CB ILE A 600 " pdb=" CA ILE A 600 " pdb=" CG1 ILE A 600 " pdb=" CG2 ILE A 600 " both_signs ideal model delta sigma weight residual False 2.64 1.93 0.71 2.00e-01 2.50e+01 1.27e+01 chirality pdb=" CA TYR A 216 " pdb=" N TYR A 216 " pdb=" C TYR A 216 " pdb=" CB TYR A 216 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.26e+00 chirality pdb=" CA GLN A 200 " pdb=" N GLN A 200 " pdb=" C GLN A 200 " pdb=" CB GLN A 200 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.13e+00 ... (remaining 1499 not shown) Planarity restraints: 1522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 239 " 0.018 2.00e-02 2.50e+03 3.60e-02 1.29e+01 pdb=" C ILE B 239 " -0.062 2.00e-02 2.50e+03 pdb=" O ILE B 239 " 0.024 2.00e-02 2.50e+03 pdb=" N ASP B 240 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 610 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.87e+00 pdb=" C ASN B 610 " 0.049 2.00e-02 2.50e+03 pdb=" O ASN B 610 " -0.019 2.00e-02 2.50e+03 pdb=" N TYR B 611 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 286 " -0.012 2.00e-02 2.50e+03 2.31e-02 5.35e+00 pdb=" C ILE B 286 " 0.040 2.00e-02 2.50e+03 pdb=" O ILE B 286 " -0.015 2.00e-02 2.50e+03 pdb=" N PHE B 287 " -0.014 2.00e-02 2.50e+03 ... (remaining 1519 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 157 2.63 - 3.20: 7878 3.20 - 3.77: 13198 3.77 - 4.33: 17537 4.33 - 4.90: 28340 Nonbonded interactions: 67110 Sorted by model distance: nonbonded pdb=" O2B AGS A 801 " pdb="MG MG A 802 " model vdw 2.063 2.170 nonbonded pdb=" O2B AGS B 801 " pdb="MG MG B 802 " model vdw 2.064 2.170 nonbonded pdb=" OG1 THR A 524 " pdb="MG MG A 802 " model vdw 2.145 2.170 nonbonded pdb=" O2G AGS B 801 " pdb="MG MG B 802 " model vdw 2.170 2.170 nonbonded pdb=" O2G AGS A 801 " pdb="MG MG A 802 " model vdw 2.171 2.170 ... (remaining 67105 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 4.040 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.430 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 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:12.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 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 : 0.011 0.079 9050 Z= 0.676 Angle : 1.384 14.404 12278 Z= 0.848 Chirality : 0.099 0.711 1502 Planarity : 0.007 0.057 1522 Dihedral : 14.892 112.635 3366 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.62 % Allowed : 5.44 % Favored : 93.94 % Rotamer: Outliers : 3.74 % Allowed : 3.13 % Favored : 93.13 % Cbeta Deviations : 0.66 % 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: -1.78 (0.23), residues: 1122 helix: -0.60 (0.18), residues: 694 sheet: -0.01 (0.67), residues: 70 loop : -2.43 (0.28), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP B 408 HIS 0.010 0.002 HIS A 399 PHE 0.034 0.003 PHE A 468 TYR 0.021 0.002 TYR B 228 ARG 0.008 0.001 ARG B 386 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 124 time to evaluate : 1.159 Fit side-chains REVERT: A 173 LEU cc_start: 0.8835 (tp) cc_final: 0.8594 (tm) REVERT: A 201 MET cc_start: 0.7964 (mmm) cc_final: 0.7688 (mpp) REVERT: A 663 ASN cc_start: 0.9070 (m-40) cc_final: 0.8623 (m-40) REVERT: A 677 ARG cc_start: 0.8107 (mmp-170) cc_final: 0.7854 (mmp-170) REVERT: A 710 PHE cc_start: 0.8632 (t80) cc_final: 0.8177 (t80) REVERT: B 164 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8412 (mp10) REVERT: B 471 LYS cc_start: 0.8417 (mmpt) cc_final: 0.8193 (mmmt) REVERT: B 713 HIS cc_start: 0.8998 (t70) cc_final: 0.8788 (t70) outliers start: 37 outliers final: 14 residues processed: 152 average time/residue: 0.9132 time to fit residues: 151.3941 Evaluate side-chains 101 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 188 TYR Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 164 GLN Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 199 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 0.0670 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 101 optimal weight: 0.2980 overall best weight: 1.0522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN A 226 GLN B 164 GLN B 423 GLN B 490 HIS B 610 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9050 Z= 0.197 Angle : 0.642 8.561 12278 Z= 0.335 Chirality : 0.042 0.404 1502 Planarity : 0.005 0.040 1522 Dihedral : 9.751 123.743 1281 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.81 % Favored : 95.10 % Rotamer: Outliers : 4.65 % Allowed : 12.12 % Favored : 83.23 % 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 (0.24), residues: 1122 helix: 0.24 (0.19), residues: 702 sheet: -0.27 (0.63), residues: 70 loop : -2.16 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 408 HIS 0.003 0.001 HIS B 399 PHE 0.013 0.001 PHE A 382 TYR 0.016 0.001 TYR A 196 ARG 0.006 0.001 ARG B 386 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 99 time to evaluate : 1.021 Fit side-chains REVERT: A 239 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8646 (tt) REVERT: A 610 ASN cc_start: 0.7767 (m-40) cc_final: 0.7010 (t0) REVERT: A 663 ASN cc_start: 0.9029 (m-40) cc_final: 0.8614 (m-40) REVERT: A 677 ARG cc_start: 0.8075 (mmp-170) cc_final: 0.7749 (mmp-170) REVERT: A 710 PHE cc_start: 0.8510 (t80) cc_final: 0.8136 (t80) REVERT: B 326 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7700 (tpt) REVERT: B 409 MET cc_start: 0.8118 (tmm) cc_final: 0.7871 (tmm) REVERT: B 518 ILE cc_start: 0.8550 (tt) cc_final: 0.8280 (pp) outliers start: 46 outliers final: 16 residues processed: 132 average time/residue: 0.7985 time to fit residues: 116.8229 Evaluate side-chains 101 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 83 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 199 ASP Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 521 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 9.9990 chunk 31 optimal weight: 0.8980 chunk 84 optimal weight: 0.3980 chunk 69 optimal weight: 5.9990 chunk 28 optimal weight: 0.0050 chunk 101 optimal weight: 10.0000 chunk 110 optimal weight: 0.0370 chunk 90 optimal weight: 5.9990 chunk 34 optimal weight: 0.0770 chunk 81 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.2830 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9050 Z= 0.150 Angle : 0.570 9.719 12278 Z= 0.290 Chirality : 0.040 0.338 1502 Planarity : 0.004 0.031 1522 Dihedral : 8.833 127.439 1269 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.35 % Favored : 94.56 % Rotamer: Outliers : 3.33 % Allowed : 15.66 % Favored : 81.01 % 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: -0.25 (0.25), residues: 1122 helix: 0.74 (0.20), residues: 700 sheet: -0.07 (0.64), residues: 70 loop : -2.01 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 408 HIS 0.001 0.000 HIS A 490 PHE 0.012 0.001 PHE A 382 TYR 0.008 0.001 TYR A 559 ARG 0.003 0.000 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 89 time to evaluate : 1.010 Fit side-chains REVERT: A 201 MET cc_start: 0.7710 (mmm) cc_final: 0.7498 (mpp) REVERT: A 239 ILE cc_start: 0.8548 (tt) cc_final: 0.8311 (tt) REVERT: A 309 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.7631 (m-10) REVERT: A 415 MET cc_start: 0.7149 (ttp) cc_final: 0.6800 (ttm) REVERT: A 663 ASN cc_start: 0.9035 (m-40) cc_final: 0.8626 (m-40) REVERT: A 677 ARG cc_start: 0.8093 (mmp-170) cc_final: 0.7787 (mmp-170) REVERT: A 710 PHE cc_start: 0.8553 (t80) cc_final: 0.8202 (t80) REVERT: B 409 MET cc_start: 0.8070 (tmm) cc_final: 0.7750 (tmm) REVERT: B 479 LEU cc_start: 0.6004 (OUTLIER) cc_final: 0.5668 (pt) REVERT: B 518 ILE cc_start: 0.8457 (tt) cc_final: 0.8092 (pp) outliers start: 33 outliers final: 17 residues processed: 110 average time/residue: 0.8363 time to fit residues: 101.4174 Evaluate side-chains 104 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 85 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 479 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.6980 chunk 52 optimal weight: 10.0000 chunk 11 optimal weight: 0.0770 chunk 48 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 102 optimal weight: 20.0000 chunk 108 optimal weight: 10.0000 chunk 53 optimal weight: 0.2980 chunk 96 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 538 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9050 Z= 0.139 Angle : 0.535 8.197 12278 Z= 0.273 Chirality : 0.038 0.229 1502 Planarity : 0.003 0.028 1522 Dihedral : 8.455 126.671 1264 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.55 % Favored : 95.37 % Rotamer: Outliers : 3.33 % Allowed : 16.57 % Favored : 80.10 % 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: 0.23 (0.26), residues: 1122 helix: 1.11 (0.20), residues: 702 sheet: 0.03 (0.65), residues: 70 loop : -1.80 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 408 HIS 0.001 0.000 HIS A 248 PHE 0.023 0.001 PHE A 323 TYR 0.005 0.001 TYR A 559 ARG 0.002 0.000 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 91 time to evaluate : 1.030 Fit side-chains REVERT: A 201 MET cc_start: 0.7624 (mmm) cc_final: 0.7243 (mpp) REVERT: A 239 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.8141 (tt) REVERT: A 309 PHE cc_start: 0.8196 (OUTLIER) cc_final: 0.7700 (m-10) REVERT: A 663 ASN cc_start: 0.9061 (m-40) cc_final: 0.8665 (m-40) REVERT: A 677 ARG cc_start: 0.8073 (mmp-170) cc_final: 0.7762 (mmp-170) REVERT: A 710 PHE cc_start: 0.8598 (t80) cc_final: 0.8241 (t80) REVERT: B 157 PHE cc_start: 0.4574 (m-10) cc_final: 0.4344 (m-10) REVERT: B 409 MET cc_start: 0.8074 (tmm) cc_final: 0.7673 (tmm) REVERT: B 518 ILE cc_start: 0.8463 (tt) cc_final: 0.8080 (pp) outliers start: 33 outliers final: 21 residues processed: 114 average time/residue: 0.8036 time to fit residues: 101.5964 Evaluate side-chains 106 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 83 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 521 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 27 optimal weight: 0.2980 chunk 36 optimal weight: 0.0030 overall best weight: 2.0596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 HIS B 538 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9050 Z= 0.230 Angle : 0.568 7.525 12278 Z= 0.294 Chirality : 0.040 0.230 1502 Planarity : 0.004 0.049 1522 Dihedral : 8.130 124.216 1264 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.70 % Favored : 94.21 % Rotamer: Outliers : 3.64 % Allowed : 17.88 % Favored : 78.48 % 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: 0.41 (0.26), residues: 1122 helix: 1.29 (0.21), residues: 698 sheet: -0.00 (0.66), residues: 70 loop : -1.74 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 408 HIS 0.003 0.001 HIS B 713 PHE 0.016 0.001 PHE A 308 TYR 0.008 0.001 TYR B 491 ARG 0.009 0.000 ARG B 386 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 86 time to evaluate : 1.106 Fit side-chains REVERT: A 201 MET cc_start: 0.7572 (mmm) cc_final: 0.7148 (mpp) REVERT: A 239 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8393 (tt) REVERT: A 309 PHE cc_start: 0.8227 (OUTLIER) cc_final: 0.7799 (m-10) REVERT: A 663 ASN cc_start: 0.9075 (m-40) cc_final: 0.8666 (m-40) REVERT: A 677 ARG cc_start: 0.8128 (mmp-170) cc_final: 0.7915 (mmp-170) REVERT: A 710 PHE cc_start: 0.8703 (t80) cc_final: 0.8385 (t80) REVERT: B 207 ILE cc_start: 0.7997 (mm) cc_final: 0.7794 (mp) REVERT: B 409 MET cc_start: 0.8184 (tmm) cc_final: 0.7753 (tmm) REVERT: B 518 ILE cc_start: 0.8639 (tt) cc_final: 0.8298 (pp) outliers start: 36 outliers final: 21 residues processed: 111 average time/residue: 0.8199 time to fit residues: 100.4530 Evaluate side-chains 101 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 78 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 521 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 ASN B 190 GLN B 538 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 9050 Z= 0.366 Angle : 0.650 8.793 12278 Z= 0.339 Chirality : 0.043 0.194 1502 Planarity : 0.004 0.058 1522 Dihedral : 8.252 129.678 1264 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.88 % Favored : 94.03 % Rotamer: Outliers : 5.35 % Allowed : 17.68 % Favored : 76.97 % 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: 0.14 (0.26), residues: 1122 helix: 1.09 (0.21), residues: 694 sheet: -0.31 (0.65), residues: 70 loop : -1.81 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 408 HIS 0.004 0.001 HIS B 713 PHE 0.020 0.002 PHE A 308 TYR 0.014 0.001 TYR A 433 ARG 0.009 0.001 ARG B 386 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 79 time to evaluate : 1.090 Fit side-chains REVERT: A 201 MET cc_start: 0.7623 (mmm) cc_final: 0.7205 (mpp) REVERT: A 239 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8704 (tt) REVERT: A 283 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8808 (pt) REVERT: A 309 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.7806 (m-80) REVERT: A 663 ASN cc_start: 0.9071 (m-40) cc_final: 0.8701 (m-40) REVERT: A 677 ARG cc_start: 0.8146 (mmp-170) cc_final: 0.7922 (mmp-170) REVERT: A 710 PHE cc_start: 0.8821 (t80) cc_final: 0.8490 (t80) REVERT: B 190 GLN cc_start: 0.7075 (OUTLIER) cc_final: 0.6629 (tt0) REVERT: B 207 ILE cc_start: 0.7928 (mm) cc_final: 0.7686 (mp) REVERT: B 409 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.7835 (tmm) REVERT: B 518 ILE cc_start: 0.8760 (tt) cc_final: 0.8491 (pp) outliers start: 53 outliers final: 28 residues processed: 117 average time/residue: 0.8306 time to fit residues: 107.1841 Evaluate side-chains 111 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 78 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 190 GLN Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 705 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 ASN B 538 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9050 Z= 0.162 Angle : 0.564 9.526 12278 Z= 0.287 Chirality : 0.039 0.211 1502 Planarity : 0.004 0.042 1522 Dihedral : 8.097 128.772 1264 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.44 % Favored : 94.47 % Rotamer: Outliers : 2.83 % Allowed : 20.61 % Favored : 76.57 % 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: 0.40 (0.26), residues: 1122 helix: 1.27 (0.21), residues: 696 sheet: -0.29 (0.66), residues: 70 loop : -1.65 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 408 HIS 0.004 0.001 HIS B 713 PHE 0.014 0.001 PHE A 308 TYR 0.008 0.001 TYR B 491 ARG 0.010 0.000 ARG B 386 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 81 time to evaluate : 1.000 Fit side-chains REVERT: A 201 MET cc_start: 0.7580 (mmm) cc_final: 0.7182 (mpp) REVERT: A 239 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8512 (tt) REVERT: A 309 PHE cc_start: 0.8312 (OUTLIER) cc_final: 0.7850 (m-80) REVERT: A 663 ASN cc_start: 0.9027 (m-40) cc_final: 0.8666 (m-40) REVERT: A 677 ARG cc_start: 0.8134 (mmp-170) cc_final: 0.7917 (mmp-170) REVERT: A 710 PHE cc_start: 0.8704 (t80) cc_final: 0.8344 (t80) REVERT: B 207 ILE cc_start: 0.7941 (mm) cc_final: 0.7700 (mp) REVERT: B 402 LEU cc_start: 0.8706 (tm) cc_final: 0.8456 (mt) REVERT: B 518 ILE cc_start: 0.8667 (tt) cc_final: 0.8327 (pp) outliers start: 28 outliers final: 17 residues processed: 101 average time/residue: 0.8617 time to fit residues: 96.5870 Evaluate side-chains 101 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 479 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 chunk 98 optimal weight: 0.0570 chunk 103 optimal weight: 0.9990 overall best weight: 0.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 GLN B 538 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9050 Z= 0.159 Angle : 0.547 9.574 12278 Z= 0.275 Chirality : 0.038 0.178 1502 Planarity : 0.004 0.049 1522 Dihedral : 7.962 128.399 1262 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.44 % Favored : 94.47 % Rotamer: Outliers : 2.53 % Allowed : 21.82 % Favored : 75.66 % 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: 0.57 (0.26), residues: 1122 helix: 1.43 (0.21), residues: 682 sheet: -0.21 (0.66), residues: 70 loop : -1.52 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 408 HIS 0.004 0.001 HIS B 713 PHE 0.018 0.001 PHE A 308 TYR 0.006 0.001 TYR A 559 ARG 0.009 0.000 ARG B 386 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 88 time to evaluate : 1.092 Fit side-chains REVERT: A 201 MET cc_start: 0.7554 (mmm) cc_final: 0.7135 (mpp) REVERT: A 239 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8393 (tt) REVERT: A 309 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7844 (m-80) REVERT: A 663 ASN cc_start: 0.9062 (m-40) cc_final: 0.8676 (m-40) REVERT: A 677 ARG cc_start: 0.8151 (mmp-170) cc_final: 0.7940 (mmp-170) REVERT: B 207 ILE cc_start: 0.7905 (mm) cc_final: 0.7658 (mp) REVERT: B 402 LEU cc_start: 0.8668 (tm) cc_final: 0.8448 (mt) REVERT: B 518 ILE cc_start: 0.8615 (tt) cc_final: 0.8228 (pp) outliers start: 25 outliers final: 15 residues processed: 106 average time/residue: 0.8370 time to fit residues: 98.2108 Evaluate side-chains 103 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 86 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 165 ARG Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 479 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 6.9990 chunk 100 optimal weight: 0.0670 chunk 103 optimal weight: 2.9990 chunk 60 optimal weight: 20.0000 chunk 43 optimal weight: 9.9990 chunk 78 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 106 optimal weight: 7.9990 overall best weight: 1.1520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 538 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9050 Z= 0.165 Angle : 0.548 9.875 12278 Z= 0.278 Chirality : 0.039 0.347 1502 Planarity : 0.004 0.047 1522 Dihedral : 7.950 128.061 1262 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.44 % Favored : 94.47 % Rotamer: Outliers : 2.22 % Allowed : 22.73 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.26), residues: 1122 helix: 1.47 (0.21), residues: 682 sheet: -0.21 (0.66), residues: 70 loop : -1.48 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 408 HIS 0.005 0.001 HIS B 713 PHE 0.016 0.001 PHE A 308 TYR 0.006 0.001 TYR B 491 ARG 0.009 0.000 ARG B 386 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 85 time to evaluate : 0.988 Fit side-chains REVERT: A 201 MET cc_start: 0.7484 (mmm) cc_final: 0.6994 (mpp) REVERT: A 239 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8379 (tt) REVERT: A 309 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.7868 (m-10) REVERT: A 663 ASN cc_start: 0.9058 (m-40) cc_final: 0.8680 (m-40) REVERT: A 677 ARG cc_start: 0.8182 (mmp-170) cc_final: 0.7959 (mmp-170) REVERT: B 207 ILE cc_start: 0.7807 (mm) cc_final: 0.7545 (mp) REVERT: B 402 LEU cc_start: 0.8670 (tm) cc_final: 0.8458 (mt) REVERT: B 518 ILE cc_start: 0.8600 (tt) cc_final: 0.8210 (pp) outliers start: 22 outliers final: 15 residues processed: 100 average time/residue: 0.8774 time to fit residues: 96.8425 Evaluate side-chains 101 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 84 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 705 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 102 optimal weight: 8.9990 chunk 88 optimal weight: 0.0870 chunk 9 optimal weight: 0.0170 chunk 68 optimal weight: 0.6980 chunk 54 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 94 optimal weight: 8.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 GLN B 538 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9050 Z= 0.138 Angle : 0.565 10.927 12278 Z= 0.280 Chirality : 0.039 0.372 1502 Planarity : 0.004 0.045 1522 Dihedral : 7.645 125.579 1258 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.99 % Favored : 94.92 % Rotamer: Outliers : 1.72 % Allowed : 23.03 % Favored : 75.25 % 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: 0.71 (0.27), residues: 1122 helix: 1.55 (0.21), residues: 686 sheet: -0.12 (0.67), residues: 70 loop : -1.50 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 408 HIS 0.004 0.000 HIS B 713 PHE 0.022 0.001 PHE A 308 TYR 0.008 0.001 TYR A 559 ARG 0.010 0.000 ARG B 386 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 0.906 Fit side-chains REVERT: A 201 MET cc_start: 0.7452 (mmm) cc_final: 0.6853 (mpp) REVERT: A 239 ILE cc_start: 0.8389 (tt) cc_final: 0.8156 (tt) REVERT: A 309 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.7854 (m-80) REVERT: A 663 ASN cc_start: 0.9061 (m-40) cc_final: 0.8690 (m-40) REVERT: A 677 ARG cc_start: 0.8175 (mmp-170) cc_final: 0.7945 (mmp-170) REVERT: B 207 ILE cc_start: 0.7854 (mm) cc_final: 0.7579 (mp) REVERT: B 518 ILE cc_start: 0.8509 (tt) cc_final: 0.8113 (pp) outliers start: 17 outliers final: 14 residues processed: 98 average time/residue: 0.8263 time to fit residues: 89.7063 Evaluate side-chains 101 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 TYR Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 196 TYR Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 479 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.2980 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.101905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.075723 restraints weight = 17583.657| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.90 r_work: 0.3101 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9050 Z= 0.171 Angle : 0.549 11.142 12278 Z= 0.278 Chirality : 0.039 0.379 1502 Planarity : 0.004 0.048 1522 Dihedral : 7.640 126.267 1258 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.44 % Favored : 94.47 % Rotamer: Outliers : 1.72 % Allowed : 23.54 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.27), residues: 1122 helix: 1.61 (0.21), residues: 684 sheet: -0.12 (0.67), residues: 70 loop : -1.47 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 408 HIS 0.004 0.001 HIS B 713 PHE 0.020 0.001 PHE A 308 TYR 0.006 0.001 TYR B 491 ARG 0.010 0.000 ARG B 386 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2722.21 seconds wall clock time: 49 minutes 56.42 seconds (2996.42 seconds total)