Starting phenix.real_space_refine on Fri Apr 5 23:54:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrl_34977/04_2024/8hrl_34977.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrl_34977/04_2024/8hrl_34977.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrl_34977/04_2024/8hrl_34977.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrl_34977/04_2024/8hrl_34977.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrl_34977/04_2024/8hrl_34977.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hrl_34977/04_2024/8hrl_34977.pdb" } resolution = 2.8 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= -0.001 sd= 0.178 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4101 2.51 5 N 1066 2.21 5 O 1208 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 37": "OE1" <-> "OE2" Residue "A ASP 38": "OD1" <-> "OD2" Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 484": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 6412 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Chain: "E" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1542 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 183} Time building chain proxies: 3.84, per 1000 atoms: 0.60 Number of scatterers: 6412 At special positions: 0 Unit cell: (77.4, 88.58, 126.42, 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 37 16.00 O 1208 8.00 N 1066 7.00 C 4101 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.02 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " 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: 2.29 Conformation dependent library (CDL) restraints added in 1.3 seconds 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1488 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 5 sheets defined 52.0% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.635A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLN A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 80 Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 90 through 99 removed outlier: 3.590A pdb=" N ALA A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.817A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 108' Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 158 through 172 removed outlier: 3.568A pdb=" N ALA A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 194 removed outlier: 3.526A pdb=" N ALA A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 220 through 249 removed outlier: 4.080A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 300 removed outlier: 4.234A pdb=" N ASP A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.936A pdb=" N LYS A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 4.291A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 385 removed outlier: 4.557A pdb=" N LEU A 370 " --> pdb=" O MET A 366 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR A 371 " --> pdb=" O ASP A 367 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.775A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 removed outlier: 3.622A pdb=" N VAL A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 400 through 405' Processing helix chain 'A' and resid 406 through 413 removed outlier: 3.544A pdb=" N ALA A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 removed outlier: 4.192A pdb=" N SER A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.784A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 485 removed outlier: 3.880A pdb=" N TRP A 477 " --> pdb=" O TRP A 473 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 485 " --> pdb=" O LYS A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 4.635A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.845A pdb=" N CYS A 542 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 4.111A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN A 556 " --> pdb=" O GLN A 552 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 4.047A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 365 through 370 removed outlier: 3.580A pdb=" N TYR E 369 " --> pdb=" O TYR E 365 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN E 370 " --> pdb=" O SER E 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 365 through 370' Processing helix chain 'E' and resid 385 through 389 removed outlier: 3.837A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 410 removed outlier: 3.844A pdb=" N GLU E 406 " --> pdb=" O ARG E 403 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL E 407 " --> pdb=" O GLY E 404 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.294A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 349 through 352 removed outlier: 3.737A pdb=" N TRP A 349 " --> pdb=" O ARG A 357 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.527A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU E 516 " --> pdb=" O ASN E 394 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR E 396 " --> pdb=" O SER E 514 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP E 398 " --> pdb=" O VAL E 512 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TRP E 436 " --> pdb=" O ARG E 509 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'E' and resid 473 through 474 247 hydrogen bonds defined for protein. 705 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: 1.70 Time building geometry restraints manager: 2.56 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: 2065 1.34 - 1.46: 1666 1.46 - 1.58: 2802 1.58 - 1.70: 1 1.70 - 1.82: 58 Bond restraints: 6592 Sorted by residual: bond pdb=" CG PRO A 258 " pdb=" CD PRO A 258 " ideal model delta sigma weight residual 1.503 1.422 0.081 3.40e-02 8.65e+02 5.73e+00 bond pdb=" CB PRO E 499 " pdb=" CG PRO E 499 " ideal model delta sigma weight residual 1.492 1.611 -0.119 5.00e-02 4.00e+02 5.65e+00 bond pdb=" CA VAL A 364 " pdb=" CB VAL A 364 " ideal model delta sigma weight residual 1.527 1.543 -0.016 1.31e-02 5.83e+03 1.47e+00 bond pdb=" CA PHE E 338 " pdb=" CB PHE E 338 " ideal model delta sigma weight residual 1.530 1.551 -0.021 1.75e-02 3.27e+03 1.43e+00 bond pdb=" CB GLU A 160 " pdb=" CG GLU A 160 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.12e+00 ... (remaining 6587 not shown) Histogram of bond angle deviations from ideal: 93.53 - 101.65: 30 101.65 - 109.78: 825 109.78 - 117.91: 3856 117.91 - 126.03: 4107 126.03 - 134.16: 140 Bond angle restraints: 8958 Sorted by residual: angle pdb=" CA PRO E 499 " pdb=" N PRO E 499 " pdb=" CD PRO E 499 " ideal model delta sigma weight residual 112.00 99.45 12.55 1.40e+00 5.10e-01 8.04e+01 angle pdb=" N PRO A 258 " pdb=" CD PRO A 258 " pdb=" CG PRO A 258 " ideal model delta sigma weight residual 103.20 93.53 9.67 1.50e+00 4.44e-01 4.16e+01 angle pdb=" CA PRO A 258 " pdb=" N PRO A 258 " pdb=" CD PRO A 258 " ideal model delta sigma weight residual 112.00 103.88 8.12 1.40e+00 5.10e-01 3.36e+01 angle pdb=" CA GLU A 160 " pdb=" CB GLU A 160 " pdb=" CG GLU A 160 " ideal model delta sigma weight residual 114.10 122.69 -8.59 2.00e+00 2.50e-01 1.84e+01 angle pdb=" CA PRO A 258 " pdb=" CB PRO A 258 " pdb=" CG PRO A 258 " ideal model delta sigma weight residual 104.50 97.12 7.38 1.90e+00 2.77e-01 1.51e+01 ... (remaining 8953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 3268 17.52 - 35.04: 444 35.04 - 52.56: 144 52.56 - 70.08: 26 70.08 - 87.60: 11 Dihedral angle restraints: 3893 sinusoidal: 1573 harmonic: 2320 Sorted by residual: dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual 93.00 156.69 -63.69 1 1.00e+01 1.00e-02 5.34e+01 dihedral pdb=" CB CYS E 391 " pdb=" SG CYS E 391 " pdb=" SG CYS E 525 " pdb=" CB CYS E 525 " ideal model delta sinusoidal sigma weight residual -86.00 -24.34 -61.66 1 1.00e+01 1.00e-02 5.04e+01 dihedral pdb=" CB CYS A 344 " pdb=" SG CYS A 344 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 133.78 -40.78 1 1.00e+01 1.00e-02 2.33e+01 ... (remaining 3890 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 546 0.035 - 0.069: 278 0.069 - 0.103: 80 0.103 - 0.138: 27 0.138 - 0.172: 3 Chirality restraints: 934 Sorted by residual: chirality pdb=" CA ASP A 509 " pdb=" N ASP A 509 " pdb=" C ASP A 509 " pdb=" CB ASP A 509 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.44e-01 chirality pdb=" CA LYS A 234 " pdb=" N LYS A 234 " pdb=" C LYS A 234 " pdb=" CB LYS A 234 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CA ILE E 410 " pdb=" N ILE E 410 " pdb=" C ILE E 410 " pdb=" CB ILE E 410 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 931 not shown) Planarity restraints: 1165 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN E 498 " 0.106 5.00e-02 4.00e+02 1.51e-01 3.63e+01 pdb=" N PRO E 499 " -0.260 5.00e-02 4.00e+02 pdb=" CA PRO E 499 " 0.077 5.00e-02 4.00e+02 pdb=" CD PRO E 499 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 257 " 0.048 5.00e-02 4.00e+02 6.83e-02 7.47e+00 pdb=" N PRO A 258 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 258 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 258 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 320 " -0.031 5.00e-02 4.00e+02 4.74e-02 3.59e+00 pdb=" N PRO A 321 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 321 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 321 " -0.026 5.00e-02 4.00e+02 ... (remaining 1162 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 105 2.68 - 3.23: 5701 3.23 - 3.79: 9299 3.79 - 4.34: 12440 4.34 - 4.90: 21104 Nonbonded interactions: 48649 Sorted by model distance: nonbonded pdb=" O PHE A 327 " pdb=" OG SER A 331 " model vdw 2.124 2.440 nonbonded pdb=" NH1 ARG E 346 " pdb=" O PHE E 347 " model vdw 2.185 2.520 nonbonded pdb=" OG SER E 371 " pdb=" OG SER E 373 " model vdw 2.262 2.440 nonbonded pdb=" O THR A 118 " pdb=" OG1 THR A 122 " model vdw 2.264 2.440 nonbonded pdb=" O LEU A 143 " pdb=" N LEU A 148 " model vdw 2.276 2.520 ... (remaining 48644 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 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: 7.410 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 20.880 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 6592 Z= 0.259 Angle : 0.733 12.552 8958 Z= 0.410 Chirality : 0.045 0.172 934 Planarity : 0.007 0.151 1165 Dihedral : 18.125 87.601 2384 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.59 % Allowed : 27.52 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -1.16 (0.28), residues: 787 helix: 0.21 (0.28), residues: 348 sheet: -1.45 (0.70), residues: 50 loop : -1.58 (0.28), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 473 HIS 0.007 0.001 HIS A 241 PHE 0.022 0.002 PHE A 592 TYR 0.018 0.002 TYR A 279 ARG 0.004 0.001 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 0.765 Fit side-chains REVERT: A 297 MET cc_start: 0.0877 (ttt) cc_final: -0.0262 (mtm) REVERT: A 316 VAL cc_start: 0.7139 (t) cc_final: 0.6831 (t) REVERT: A 536 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6609 (mp0) outliers start: 11 outliers final: 8 residues processed: 84 average time/residue: 1.0589 time to fit residues: 94.5080 Evaluate side-chains 77 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 68 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 424 LYS Chi-restraints excluded: chain E residue 503 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.0970 chunk 59 optimal weight: 3.9990 chunk 32 optimal weight: 0.0670 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 0.3980 chunk 31 optimal weight: 0.0870 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 45 optimal weight: 0.4980 chunk 70 optimal weight: 4.9990 overall best weight: 0.2294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 437 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6592 Z= 0.131 Angle : 0.489 8.562 8958 Z= 0.257 Chirality : 0.040 0.132 934 Planarity : 0.004 0.083 1165 Dihedral : 4.965 41.858 876 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.31 % Allowed : 25.36 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.59 (0.29), residues: 787 helix: 0.64 (0.29), residues: 345 sheet: -1.15 (0.74), residues: 50 loop : -1.22 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 473 HIS 0.003 0.001 HIS A 417 PHE 0.017 0.001 PHE E 486 TYR 0.010 0.001 TYR A 510 ARG 0.001 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 74 time to evaluate : 0.722 Fit side-chains REVERT: A 79 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7800 (tt) REVERT: A 297 MET cc_start: 0.1112 (ttt) cc_final: 0.0600 (ptm) REVERT: A 313 LYS cc_start: 0.6737 (mmtp) cc_final: 0.6177 (mtmm) REVERT: A 406 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7014 (mm-30) outliers start: 23 outliers final: 7 residues processed: 92 average time/residue: 1.0785 time to fit residues: 105.3641 Evaluate side-chains 74 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 562 LYS Chi-restraints excluded: chain A residue 611 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 19 optimal weight: 0.0970 chunk 70 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 56 optimal weight: 0.0570 chunk 53 optimal weight: 0.9990 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 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 HIS E 474 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6592 Z= 0.156 Angle : 0.506 7.973 8958 Z= 0.267 Chirality : 0.041 0.171 934 Planarity : 0.004 0.062 1165 Dihedral : 4.109 28.025 862 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.32 % Allowed : 24.93 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.51 (0.29), residues: 787 helix: 0.72 (0.29), residues: 344 sheet: -0.85 (0.76), residues: 50 loop : -1.24 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 473 HIS 0.005 0.001 HIS A 241 PHE 0.012 0.001 PHE E 486 TYR 0.015 0.001 TYR A 385 ARG 0.001 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 69 time to evaluate : 0.665 Fit side-chains REVERT: A 89 GLN cc_start: 0.6919 (OUTLIER) cc_final: 0.6460 (mp10) REVERT: A 171 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7077 (mp0) REVERT: A 297 MET cc_start: 0.1136 (ttt) cc_final: 0.0151 (mtt) REVERT: A 406 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7161 (mm-30) REVERT: A 552 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7348 (mp10) REVERT: A 562 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7453 (mttt) REVERT: E 474 GLN cc_start: 0.5300 (tt0) cc_final: 0.4919 (tm-30) outliers start: 30 outliers final: 12 residues processed: 89 average time/residue: 1.1617 time to fit residues: 109.1006 Evaluate side-chains 81 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 64 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 552 GLN Chi-restraints excluded: chain A residue 562 LYS Chi-restraints excluded: chain E residue 424 LYS Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 503 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 0.0010 chunk 71 optimal weight: 0.4980 chunk 75 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 53 ASN ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6592 Z= 0.164 Angle : 0.529 12.409 8958 Z= 0.276 Chirality : 0.041 0.174 934 Planarity : 0.004 0.050 1165 Dihedral : 4.036 17.187 861 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 5.48 % Allowed : 24.93 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.52 (0.29), residues: 787 helix: 0.73 (0.29), residues: 345 sheet: -0.71 (0.76), residues: 50 loop : -1.29 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 473 HIS 0.005 0.001 HIS A 241 PHE 0.010 0.001 PHE E 486 TYR 0.015 0.001 TYR A 385 ARG 0.002 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 69 time to evaluate : 0.814 Fit side-chains REVERT: A 89 GLN cc_start: 0.6876 (OUTLIER) cc_final: 0.6475 (mp10) REVERT: A 171 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7050 (mp0) REVERT: A 297 MET cc_start: 0.0989 (OUTLIER) cc_final: 0.0116 (mtm) REVERT: A 406 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7131 (mm-30) REVERT: A 552 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7376 (mp10) REVERT: A 562 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7467 (mttt) REVERT: E 474 GLN cc_start: 0.5286 (tt0) cc_final: 0.4900 (tm-30) REVERT: E 513 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6761 (tm) outliers start: 38 outliers final: 17 residues processed: 94 average time/residue: 1.1550 time to fit residues: 115.0770 Evaluate side-chains 90 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 66 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 552 GLN Chi-restraints excluded: chain A residue 562 LYS Chi-restraints excluded: chain E residue 424 LYS Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain E residue 523 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 52 optimal weight: 0.0770 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 67 optimal weight: 0.0870 chunk 19 optimal weight: 0.3980 chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6592 Z= 0.138 Angle : 0.506 9.504 8958 Z= 0.256 Chirality : 0.040 0.174 934 Planarity : 0.004 0.045 1165 Dihedral : 3.793 15.537 861 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.61 % Allowed : 25.94 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.34 (0.29), residues: 787 helix: 0.93 (0.29), residues: 348 sheet: -0.57 (0.76), residues: 50 loop : -1.27 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 477 HIS 0.004 0.001 HIS A 241 PHE 0.014 0.001 PHE E 338 TYR 0.014 0.001 TYR A 279 ARG 0.003 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 69 time to evaluate : 0.715 Fit side-chains revert: symmetry clash REVERT: A 171 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7047 (mp0) REVERT: A 259 ILE cc_start: 0.6382 (OUTLIER) cc_final: 0.6169 (mm) REVERT: A 297 MET cc_start: 0.0788 (ttt) cc_final: 0.0020 (mtm) REVERT: A 369 PHE cc_start: 0.4047 (OUTLIER) cc_final: 0.3842 (m-80) REVERT: A 552 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7352 (mp10) REVERT: A 562 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7433 (mttt) REVERT: E 474 GLN cc_start: 0.5188 (tt0) cc_final: 0.4807 (tm-30) outliers start: 32 outliers final: 18 residues processed: 94 average time/residue: 1.0683 time to fit residues: 106.5034 Evaluate side-chains 87 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 64 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 369 PHE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 552 GLN Chi-restraints excluded: chain A residue 562 LYS Chi-restraints excluded: chain E residue 424 LYS Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 523 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 62 optimal weight: 0.0060 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 51 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6592 Z= 0.210 Angle : 0.574 9.135 8958 Z= 0.300 Chirality : 0.043 0.197 934 Planarity : 0.005 0.043 1165 Dihedral : 4.189 19.328 861 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.47 % Allowed : 26.22 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.53 (0.29), residues: 787 helix: 0.73 (0.28), residues: 346 sheet: -0.29 (0.78), residues: 48 loop : -1.37 (0.28), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 473 HIS 0.008 0.001 HIS A 241 PHE 0.033 0.002 PHE E 338 TYR 0.021 0.002 TYR A 279 ARG 0.004 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 71 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: A 89 GLN cc_start: 0.6813 (OUTLIER) cc_final: 0.6379 (mp10) REVERT: A 171 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7095 (mp0) REVERT: A 259 ILE cc_start: 0.6592 (OUTLIER) cc_final: 0.6352 (mm) REVERT: A 297 MET cc_start: 0.1082 (OUTLIER) cc_final: 0.0206 (mtp) REVERT: A 367 ASP cc_start: 0.4944 (OUTLIER) cc_final: 0.4508 (m-30) REVERT: A 369 PHE cc_start: 0.4322 (OUTLIER) cc_final: 0.3546 (m-80) REVERT: A 406 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7086 (mm-30) REVERT: A 552 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7450 (mp10) REVERT: A 562 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7561 (mttt) outliers start: 31 outliers final: 15 residues processed: 90 average time/residue: 1.0763 time to fit residues: 102.7365 Evaluate side-chains 90 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 66 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 369 PHE Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 552 GLN Chi-restraints excluded: chain A residue 562 LYS Chi-restraints excluded: chain E residue 424 LYS Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 523 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 47 optimal weight: 0.0970 chunk 45 optimal weight: 0.7980 chunk 34 optimal weight: 0.2980 chunk 46 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS E 474 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6592 Z= 0.143 Angle : 0.501 7.659 8958 Z= 0.259 Chirality : 0.040 0.174 934 Planarity : 0.004 0.038 1165 Dihedral : 3.903 18.616 861 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.32 % Allowed : 26.22 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.29 (0.29), residues: 787 helix: 0.95 (0.29), residues: 348 sheet: -0.20 (0.76), residues: 49 loop : -1.27 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 69 HIS 0.005 0.001 HIS A 241 PHE 0.017 0.001 PHE E 338 TYR 0.020 0.001 TYR A 279 ARG 0.002 0.000 ARG E 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 73 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: A 89 GLN cc_start: 0.6807 (OUTLIER) cc_final: 0.6344 (mp10) REVERT: A 171 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7060 (mp0) REVERT: A 259 ILE cc_start: 0.6610 (OUTLIER) cc_final: 0.6358 (mm) REVERT: A 291 ILE cc_start: 0.2297 (OUTLIER) cc_final: 0.1542 (mp) REVERT: A 297 MET cc_start: 0.1007 (OUTLIER) cc_final: -0.0006 (mtm) REVERT: A 369 PHE cc_start: 0.4172 (OUTLIER) cc_final: 0.3754 (m-80) REVERT: A 406 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7187 (mm-30) REVERT: A 552 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7402 (mp10) outliers start: 30 outliers final: 19 residues processed: 93 average time/residue: 1.1155 time to fit residues: 110.0166 Evaluate side-chains 95 residues out of total 694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 68 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 163 TRP Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 369 PHE Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 552 GLN Chi-restraints excluded: chain A residue 562 LYS Chi-restraints excluded: chain E residue 424 LYS Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain E residue 523 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.2697 > 50: distance: 102 - 107: 22.391 distance: 107 - 108: 33.706 distance: 108 - 109: 45.589 distance: 108 - 111: 6.043 distance: 109 - 110: 25.837 distance: 109 - 114: 25.943 distance: 111 - 112: 37.049 distance: 111 - 113: 20.468 distance: 114 - 115: 35.791 distance: 115 - 116: 9.235 distance: 115 - 118: 32.896 distance: 116 - 117: 44.199 distance: 116 - 123: 25.284 distance: 118 - 119: 22.132 distance: 119 - 120: 17.193 distance: 120 - 121: 19.337 distance: 120 - 122: 14.932 distance: 123 - 124: 32.139 distance: 123 - 129: 22.109 distance: 124 - 125: 25.677 distance: 124 - 127: 31.171 distance: 125 - 126: 13.787 distance: 125 - 130: 27.471 distance: 127 - 128: 21.352 distance: 128 - 129: 6.631 distance: 130 - 131: 18.513 distance: 131 - 132: 36.836 distance: 131 - 134: 22.818 distance: 132 - 133: 33.282 distance: 132 - 137: 43.975 distance: 134 - 135: 23.704 distance: 134 - 136: 21.447 distance: 137 - 138: 21.977 distance: 137 - 143: 32.382 distance: 138 - 139: 20.645 distance: 138 - 141: 15.880 distance: 139 - 140: 32.897 distance: 139 - 144: 18.736 distance: 141 - 142: 7.494 distance: 142 - 143: 6.847 distance: 144 - 145: 51.361 distance: 145 - 146: 60.270 distance: 145 - 148: 28.251 distance: 146 - 147: 29.904 distance: 146 - 154: 35.942 distance: 148 - 149: 37.848 distance: 149 - 150: 20.384 distance: 149 - 151: 27.047 distance: 150 - 152: 16.644 distance: 151 - 153: 13.118 distance: 152 - 153: 32.940 distance: 154 - 155: 53.471 distance: 155 - 156: 51.099 distance: 155 - 158: 37.162 distance: 156 - 157: 35.453 distance: 156 - 162: 39.686 distance: 158 - 159: 33.066 distance: 159 - 160: 21.865 distance: 159 - 161: 14.292 distance: 162 - 163: 26.128 distance: 163 - 164: 35.615 distance: 163 - 166: 42.377 distance: 164 - 165: 38.178 distance: 164 - 171: 16.300 distance: 166 - 167: 23.148 distance: 167 - 168: 18.318 distance: 168 - 169: 21.546 distance: 168 - 170: 15.763 distance: 171 - 172: 42.607 distance: 172 - 173: 35.472 distance: 172 - 175: 35.791 distance: 173 - 174: 14.707 distance: 173 - 178: 18.726 distance: 175 - 176: 46.765 distance: 175 - 177: 39.878 distance: 178 - 179: 21.363 distance: 179 - 180: 18.991 distance: 179 - 182: 33.402 distance: 180 - 181: 25.303 distance: 180 - 190: 20.682 distance: 182 - 183: 15.618 distance: 183 - 184: 9.486 distance: 183 - 185: 12.327 distance: 184 - 186: 15.464 distance: 185 - 187: 14.728 distance: 186 - 188: 17.922 distance: 187 - 188: 18.081 distance: 188 - 189: 13.152