Starting phenix.real_space_refine on Wed Sep 25 22:43:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrj_14916/09_2024/7zrj_14916.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrj_14916/09_2024/7zrj_14916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrj_14916/09_2024/7zrj_14916.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrj_14916/09_2024/7zrj_14916.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrj_14916/09_2024/7zrj_14916.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrj_14916/09_2024/7zrj_14916.cif" } resolution = 3.7 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= 0.005 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: 6 Type Number sf(0) Gaussians K 7 8.98 5 P 5 5.49 5 S 62 5.16 5 C 7120 2.51 5 N 1821 2.21 5 O 1994 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 11009 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4155 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain: "C" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1431 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 13, 'TRANS': 176} Chain: "D" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 200 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "B" Number of atoms: 5016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5016 Classifications: {'peptide': 675} Link IDs: {'PTRANS': 26, 'TRANS': 648} Chain: "A" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 206 Unusual residues: {' K': 6, 'CDL': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.91, per 1000 atoms: 0.72 Number of scatterers: 11009 At special positions: 0 Unit cell: (98.164, 112.332, 153.824, 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) K 7 19.00 S 62 16.00 P 5 15.00 O 1994 8.00 N 1821 7.00 C 7120 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 - 3.00 Amino acid : True - 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: 3.34 Conformation dependent library (CDL) restraints added in 1.7 seconds 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2636 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 10 sheets defined 62.8% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 1 through 32 Proline residue: A 22 - end of helix removed outlier: 3.624A pdb=" N SER A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLY A 26 " --> pdb=" O PRO A 22 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ARG A 29 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 30 " --> pdb=" O GLY A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 51 removed outlier: 3.898A pdb=" N ARG A 48 " --> pdb=" O ARG A 44 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA A 49 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 82 Processing helix chain 'A' and resid 98 through 111 Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 125 through 131 removed outlier: 3.742A pdb=" N GLN A 129 " --> pdb=" O SER A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 157 removed outlier: 3.576A pdb=" N GLN A 136 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ALA A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 177 Processing helix chain 'A' and resid 179 through 193 Processing helix chain 'A' and resid 218 through 228 removed outlier: 3.791A pdb=" N GLN A 222 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 274 removed outlier: 4.606A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Proline residue: A 263 - end of helix removed outlier: 3.838A pdb=" N MET A 274 " --> pdb=" O PHE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 305 removed outlier: 4.023A pdb=" N LEU A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.914A pdb=" N ALA A 311 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 342 Processing helix chain 'A' and resid 350 through 354 removed outlier: 3.533A pdb=" N PHE A 354 " --> pdb=" O HIS A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 368 removed outlier: 3.788A pdb=" N VAL A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 377 through 399 removed outlier: 3.688A pdb=" N TYR A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N MET A 383 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE A 386 " --> pdb=" O GLY A 382 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 435 removed outlier: 4.650A pdb=" N LEU A 416 " --> pdb=" O ARG A 412 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N THR A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.797A pdb=" N ARG A 442 " --> pdb=" O THR A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 465 removed outlier: 4.064A pdb=" N PHE A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 495 Processing helix chain 'A' and resid 496 through 510 removed outlier: 4.020A pdb=" N SER A 509 " --> pdb=" O GLY A 505 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 538 Processing helix chain 'A' and resid 543 through 549 removed outlier: 4.165A pdb=" N LEU A 549 " --> pdb=" O PRO A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 556 Processing helix chain 'C' and resid 3 through 19 Processing helix chain 'C' and resid 21 through 34 removed outlier: 3.535A pdb=" N TRP C 32 " --> pdb=" O VAL C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 39 Processing helix chain 'C' and resid 91 through 109 Processing helix chain 'C' and resid 133 through 140 removed outlier: 3.910A pdb=" N GLN C 140 " --> pdb=" O ALA C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 149 Processing helix chain 'C' and resid 151 through 162 Processing helix chain 'C' and resid 178 through 190 Processing helix chain 'D' and resid 5 through 25 Processing helix chain 'B' and resid 14 through 22 Processing helix chain 'B' and resid 26 through 30 Processing helix chain 'B' and resid 33 through 56 removed outlier: 4.200A pdb=" N VAL B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 99 removed outlier: 4.108A pdb=" N GLY B 99 " --> pdb=" O ASN B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 160 Processing helix chain 'B' and resid 198 through 210 Processing helix chain 'B' and resid 215 through 246 removed outlier: 4.403A pdb=" N TRP B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) Proline residue: B 241 - end of helix removed outlier: 3.718A pdb=" N GLY B 246 " --> pdb=" O PHE B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 263 Processing helix chain 'B' and resid 264 through 271 Processing helix chain 'B' and resid 272 through 285 removed outlier: 5.977A pdb=" N GLY B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 300 Processing helix chain 'B' and resid 307 through 311 removed outlier: 3.578A pdb=" N GLY B 310 " --> pdb=" O ASN B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 342 Processing helix chain 'B' and resid 346 through 360 Processing helix chain 'B' and resid 397 through 408 Processing helix chain 'B' and resid 413 through 427 removed outlier: 4.143A pdb=" N ASP B 417 " --> pdb=" O PRO B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 463 Processing helix chain 'B' and resid 474 through 484 Processing helix chain 'B' and resid 495 through 509 Processing helix chain 'B' and resid 522 through 529 Processing helix chain 'B' and resid 539 through 546 Processing helix chain 'B' and resid 554 through 556 No H-bonds generated for 'chain 'B' and resid 554 through 556' Processing helix chain 'B' and resid 557 through 582 removed outlier: 3.621A pdb=" N LEU B 569 " --> pdb=" O GLY B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 595 Proline residue: B 592 - end of helix Processing helix chain 'B' and resid 599 through 605 removed outlier: 4.135A pdb=" N ALA B 604 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 637 removed outlier: 3.782A pdb=" N ILE B 617 " --> pdb=" O PRO B 613 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU B 618 " --> pdb=" O ASP B 614 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) Proline residue: B 633 - end of helix Processing helix chain 'B' and resid 645 through 661 removed outlier: 4.372A pdb=" N LEU B 659 " --> pdb=" O TRP B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 680 Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 205 Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 44 removed outlier: 3.874A pdb=" N GLY C 51 " --> pdb=" O ILE C 43 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 131 through 132 Processing sheet with id=AA5, first strand: chain 'B' and resid 131 through 134 Processing sheet with id=AA6, first strand: chain 'B' and resid 138 through 139 Processing sheet with id=AA7, first strand: chain 'B' and resid 152 through 155 removed outlier: 6.103A pdb=" N VAL B 153 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA B 163 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU B 155 " --> pdb=" O GLU B 161 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU B 161 " --> pdb=" O GLU B 155 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 287 through 289 Processing sheet with id=AA9, first strand: chain 'B' and resid 489 through 491 removed outlier: 6.670A pdb=" N THR B 467 " --> pdb=" O ASP B 489 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N LEU B 491 " --> pdb=" O THR B 467 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N MET B 469 " --> pdb=" O LEU B 491 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 393 through 396 removed outlier: 6.262A pdb=" N VAL B 433 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU B 435 " --> pdb=" O ARG B 438 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG B 438 " --> pdb=" O GLU B 435 " (cutoff:3.500A) 637 hydrogen bonds defined for protein. 1869 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: 3.28 Time building geometry restraints manager: 3.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1859 1.32 - 1.45: 2669 1.45 - 1.57: 6548 1.57 - 1.69: 12 1.69 - 1.82: 112 Bond restraints: 11200 Sorted by residual: bond pdb=" OA3 CDL A 607 " pdb=" PA1 CDL A 607 " ideal model delta sigma weight residual 1.529 1.502 0.027 1.00e-02 1.00e+04 7.20e+00 bond pdb=" OA3 CDL A 608 " pdb=" PA1 CDL A 608 " ideal model delta sigma weight residual 1.529 1.503 0.026 1.00e-02 1.00e+04 6.95e+00 bond pdb=" N ASP C 111 " pdb=" CA ASP C 111 " ideal model delta sigma weight residual 1.454 1.489 -0.034 1.31e-02 5.83e+03 6.86e+00 bond pdb=" OB3 CDL A 608 " pdb=" PB2 CDL A 608 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.27e+00 bond pdb=" OB3 CDL A 607 " pdb=" PB2 CDL A 607 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.11e+00 ... (remaining 11195 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 14796 2.14 - 4.29: 313 4.29 - 6.43: 63 6.43 - 8.57: 19 8.57 - 10.72: 6 Bond angle restraints: 15197 Sorted by residual: angle pdb=" C GLY A 83 " pdb=" N GLN A 84 " pdb=" CA GLN A 84 " ideal model delta sigma weight residual 121.54 130.84 -9.30 1.91e+00 2.74e-01 2.37e+01 angle pdb=" N GLU B 544 " pdb=" CA GLU B 544 " pdb=" CB GLU B 544 " ideal model delta sigma weight residual 110.28 117.15 -6.87 1.55e+00 4.16e-01 1.96e+01 angle pdb=" CA GLU B 544 " pdb=" CB GLU B 544 " pdb=" CG GLU B 544 " ideal model delta sigma weight residual 114.10 122.69 -8.59 2.00e+00 2.50e-01 1.84e+01 angle pdb=" CB MET A 227 " pdb=" CG MET A 227 " pdb=" SD MET A 227 " ideal model delta sigma weight residual 112.70 123.42 -10.72 3.00e+00 1.11e-01 1.28e+01 angle pdb=" CA TYR A 381 " pdb=" CB TYR A 381 " pdb=" CG TYR A 381 " ideal model delta sigma weight residual 113.90 120.24 -6.34 1.80e+00 3.09e-01 1.24e+01 ... (remaining 15192 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 5880 17.26 - 34.51: 636 34.51 - 51.77: 156 51.77 - 69.02: 45 69.02 - 86.28: 15 Dihedral angle restraints: 6732 sinusoidal: 2629 harmonic: 4103 Sorted by residual: dihedral pdb=" CA ALA A 470 " pdb=" C ALA A 470 " pdb=" N PHE A 471 " pdb=" CA PHE A 471 " ideal model delta harmonic sigma weight residual 180.00 151.28 28.72 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA PHE A 373 " pdb=" C PHE A 373 " pdb=" N GLY A 374 " pdb=" CA GLY A 374 " ideal model delta harmonic sigma weight residual -180.00 -159.42 -20.58 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA ILE B 656 " pdb=" C ILE B 656 " pdb=" N TYR B 657 " pdb=" CA TYR B 657 " ideal model delta harmonic sigma weight residual -180.00 -160.57 -19.43 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 6729 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1433 0.058 - 0.116: 332 0.116 - 0.174: 39 0.174 - 0.233: 3 0.233 - 0.291: 3 Chirality restraints: 1810 Sorted by residual: chirality pdb=" CG LEU A 170 " pdb=" CB LEU A 170 " pdb=" CD1 LEU A 170 " pdb=" CD2 LEU A 170 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CB ILE B 386 " pdb=" CA ILE B 386 " pdb=" CG1 ILE B 386 " pdb=" CG2 ILE B 386 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CB VAL C 175 " pdb=" CA VAL C 175 " pdb=" CG1 VAL C 175 " pdb=" CG2 VAL C 175 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 1807 not shown) Planarity restraints: 1908 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU C 153 " 0.011 2.00e-02 2.50e+03 2.33e-02 5.45e+00 pdb=" CD GLU C 153 " -0.040 2.00e-02 2.50e+03 pdb=" OE1 GLU C 153 " 0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU C 153 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 116 " 0.037 5.00e-02 4.00e+02 5.68e-02 5.16e+00 pdb=" N PRO C 117 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 117 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 117 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 133 " -0.036 5.00e-02 4.00e+02 5.51e-02 4.85e+00 pdb=" N PRO C 134 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 134 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 134 " -0.031 5.00e-02 4.00e+02 ... (remaining 1905 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.77: 2044 2.77 - 3.36: 12829 3.36 - 3.96: 21825 3.96 - 4.55: 30073 4.55 - 5.14: 44847 Nonbonded interactions: 111618 Sorted by model distance: nonbonded pdb=" O ASP C 111 " pdb=" OD1 ASP C 111 " model vdw 2.179 3.040 nonbonded pdb=" O LEU A 541 " pdb=" OH TYR B 587 " model vdw 2.205 3.040 nonbonded pdb=" O THR A 248 " pdb=" OG1 THR A 251 " model vdw 2.268 3.040 nonbonded pdb=" O SER A 119 " pdb=" OG1 THR A 123 " model vdw 2.294 3.040 nonbonded pdb=" O PRO C 23 " pdb=" OG1 THR C 27 " model vdw 2.296 3.040 ... (remaining 111613 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 30.560 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 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 0.043 11200 Z= 0.258 Angle : 0.804 10.716 15197 Z= 0.406 Chirality : 0.049 0.291 1810 Planarity : 0.005 0.057 1908 Dihedral : 16.082 86.276 4096 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.20), residues: 1438 helix: -0.15 (0.17), residues: 859 sheet: -1.55 (0.79), residues: 35 loop : -1.80 (0.24), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 115 HIS 0.002 0.001 HIS B 563 PHE 0.030 0.002 PHE C 34 TYR 0.029 0.002 TYR A 381 ARG 0.009 0.000 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.218 Fit side-chains REVERT: A 176 TRP cc_start: 0.7393 (m100) cc_final: 0.7135 (m100) REVERT: A 412 ARG cc_start: 0.6980 (mmt180) cc_final: 0.6656 (mmt180) REVERT: B 303 VAL cc_start: 0.8514 (t) cc_final: 0.8105 (t) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1980 time to fit residues: 48.7670 Evaluate side-chains 129 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 112 optimal weight: 20.0000 chunk 43 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 129 optimal weight: 7.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN A 466 ASN A 467 ASN A 513 GLN ** C 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 11200 Z= 0.312 Angle : 0.628 9.891 15197 Z= 0.318 Chirality : 0.043 0.161 1810 Planarity : 0.004 0.044 1908 Dihedral : 11.109 88.327 1714 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.15 % Allowed : 9.25 % Favored : 89.60 % 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: -0.39 (0.22), residues: 1438 helix: 0.62 (0.18), residues: 867 sheet: -1.60 (0.70), residues: 49 loop : -1.59 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 655 HIS 0.004 0.001 HIS A 451 PHE 0.019 0.002 PHE A 373 TYR 0.021 0.002 TYR A 458 ARG 0.004 0.000 ARG B 394 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 130 time to evaluate : 1.245 Fit side-chains revert: symmetry clash REVERT: A 176 TRP cc_start: 0.7527 (m100) cc_final: 0.7240 (m100) REVERT: A 445 MET cc_start: 0.7586 (mmt) cc_final: 0.7338 (mmt) outliers start: 13 outliers final: 10 residues processed: 136 average time/residue: 0.2107 time to fit residues: 42.9038 Evaluate side-chains 131 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 121 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 626 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 108 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 140 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 chunk 129 optimal weight: 9.9990 chunk 44 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 157 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11200 Z= 0.223 Angle : 0.570 7.814 15197 Z= 0.287 Chirality : 0.041 0.147 1810 Planarity : 0.004 0.044 1908 Dihedral : 10.568 85.455 1714 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.59 % Allowed : 12.07 % Favored : 86.34 % 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: -0.00 (0.22), residues: 1438 helix: 0.98 (0.18), residues: 865 sheet: -1.34 (0.70), residues: 51 loop : -1.52 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 115 HIS 0.004 0.001 HIS A 451 PHE 0.014 0.001 PHE B 173 TYR 0.020 0.002 TYR A 381 ARG 0.004 0.000 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 134 time to evaluate : 1.230 Fit side-chains revert: symmetry clash REVERT: A 176 TRP cc_start: 0.7447 (m100) cc_final: 0.7180 (m100) REVERT: A 445 MET cc_start: 0.7870 (mmt) cc_final: 0.7129 (mmt) REVERT: C 93 GLU cc_start: 0.8161 (tp30) cc_final: 0.7951 (tp30) REVERT: B 469 MET cc_start: 0.6832 (ttt) cc_final: 0.6512 (mtp) outliers start: 18 outliers final: 10 residues processed: 143 average time/residue: 0.2289 time to fit residues: 48.9163 Evaluate side-chains 131 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 121 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 526 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 138 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 157 GLN B 603 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11200 Z= 0.237 Angle : 0.577 9.020 15197 Z= 0.289 Chirality : 0.041 0.145 1810 Planarity : 0.004 0.043 1908 Dihedral : 10.205 83.014 1714 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.38 % Allowed : 14.36 % Favored : 83.26 % 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: 0.10 (0.22), residues: 1438 helix: 1.06 (0.18), residues: 864 sheet: -1.00 (0.71), residues: 49 loop : -1.49 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 115 HIS 0.003 0.001 HIS A 451 PHE 0.014 0.001 PHE A 373 TYR 0.019 0.002 TYR A 381 ARG 0.002 0.000 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 125 time to evaluate : 1.238 Fit side-chains revert: symmetry clash REVERT: A 176 TRP cc_start: 0.7453 (m100) cc_final: 0.7204 (m100) REVERT: C 93 GLU cc_start: 0.8190 (tp30) cc_final: 0.7869 (tp30) REVERT: B 469 MET cc_start: 0.6810 (ttt) cc_final: 0.6578 (mtp) outliers start: 27 outliers final: 15 residues processed: 143 average time/residue: 0.2091 time to fit residues: 45.1090 Evaluate side-chains 131 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 116 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 603 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 9.9990 chunk 78 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 102 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 chunk 117 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 chunk 124 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11200 Z= 0.231 Angle : 0.583 11.924 15197 Z= 0.290 Chirality : 0.041 0.153 1810 Planarity : 0.004 0.042 1908 Dihedral : 9.901 81.747 1714 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.64 % Allowed : 14.71 % Favored : 82.64 % 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: 0.21 (0.22), residues: 1438 helix: 1.15 (0.18), residues: 859 sheet: -0.84 (0.72), residues: 49 loop : -1.46 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 115 HIS 0.003 0.001 HIS A 451 PHE 0.013 0.001 PHE A 373 TYR 0.019 0.002 TYR A 381 ARG 0.004 0.000 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 124 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 TRP cc_start: 0.7471 (m100) cc_final: 0.7214 (m100) REVERT: A 256 MET cc_start: 0.8143 (mtt) cc_final: 0.7726 (mtt) REVERT: A 445 MET cc_start: 0.8330 (mmt) cc_final: 0.7695 (mmt) REVERT: C 93 GLU cc_start: 0.8197 (tp30) cc_final: 0.7976 (tp30) REVERT: B 469 MET cc_start: 0.6841 (ttt) cc_final: 0.6620 (mtp) outliers start: 30 outliers final: 21 residues processed: 143 average time/residue: 0.1941 time to fit residues: 41.7919 Evaluate side-chains 136 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 115 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 549 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 4.9990 chunk 124 optimal weight: 0.0970 chunk 27 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 34 optimal weight: 0.5980 chunk 138 optimal weight: 0.7980 chunk 114 optimal weight: 8.9990 chunk 64 optimal weight: 0.0170 chunk 11 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11200 Z= 0.143 Angle : 0.553 12.713 15197 Z= 0.271 Chirality : 0.040 0.153 1810 Planarity : 0.004 0.043 1908 Dihedral : 9.185 83.184 1714 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.03 % Allowed : 15.51 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.23), residues: 1438 helix: 1.28 (0.18), residues: 867 sheet: -0.70 (0.72), residues: 49 loop : -1.35 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 115 HIS 0.003 0.000 HIS A 451 PHE 0.011 0.001 PHE B 173 TYR 0.022 0.001 TYR A 381 ARG 0.005 0.000 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 131 time to evaluate : 1.470 Fit side-chains revert: symmetry clash REVERT: A 176 TRP cc_start: 0.7483 (m100) cc_final: 0.7229 (m100) REVERT: A 445 MET cc_start: 0.8052 (mmt) cc_final: 0.7513 (mmt) REVERT: B 518 ASP cc_start: 0.5814 (p0) cc_final: 0.5613 (p0) outliers start: 23 outliers final: 13 residues processed: 146 average time/residue: 0.2070 time to fit residues: 45.2878 Evaluate side-chains 135 residues out of total 1135 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 587 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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: 58.2215 > 50: distance: 17 - 38: 24.145 distance: 21 - 43: 21.991 distance: 31 - 38: 25.237 distance: 38 - 39: 20.783 distance: 39 - 40: 30.753 distance: 39 - 42: 8.791 distance: 40 - 41: 3.314 distance: 40 - 43: 28.713 distance: 43 - 44: 10.146 distance: 44 - 45: 8.943 distance: 44 - 47: 20.062 distance: 45 - 46: 16.156 distance: 45 - 51: 41.358 distance: 47 - 48: 22.684 distance: 48 - 49: 12.446 distance: 48 - 50: 29.603 distance: 51 - 52: 12.281 distance: 52 - 53: 17.542 distance: 53 - 54: 20.112 distance: 53 - 55: 14.691 distance: 55 - 56: 5.977 distance: 56 - 57: 13.348 distance: 57 - 58: 13.874 distance: 57 - 59: 33.051 distance: 59 - 60: 13.191 distance: 60 - 61: 18.341 distance: 60 - 63: 19.846 distance: 61 - 62: 31.293 distance: 61 - 69: 29.118 distance: 63 - 64: 13.408 distance: 64 - 65: 26.638 distance: 64 - 66: 10.255 distance: 65 - 67: 21.453 distance: 66 - 68: 26.053 distance: 67 - 68: 21.400 distance: 69 - 70: 25.065 distance: 70 - 71: 28.339 distance: 70 - 73: 32.473 distance: 71 - 72: 13.881 distance: 71 - 80: 18.152 distance: 73 - 74: 15.809 distance: 74 - 75: 23.064 distance: 74 - 76: 18.293 distance: 75 - 77: 11.191 distance: 76 - 78: 22.207 distance: 77 - 79: 9.690 distance: 78 - 79: 12.749 distance: 80 - 81: 18.465 distance: 80 - 86: 6.879 distance: 81 - 82: 24.193 distance: 81 - 84: 9.799 distance: 82 - 83: 25.988 distance: 82 - 87: 30.680 distance: 84 - 85: 26.615 distance: 85 - 86: 22.960 distance: 87 - 88: 8.396 distance: 88 - 89: 5.843 distance: 88 - 91: 10.282 distance: 89 - 90: 11.796 distance: 89 - 94: 9.773 distance: 90 - 117: 14.502 distance: 91 - 92: 15.423 distance: 91 - 93: 4.837 distance: 94 - 95: 12.057 distance: 95 - 96: 5.804 distance: 95 - 98: 9.204 distance: 96 - 97: 8.643 distance: 96 - 102: 3.527 distance: 97 - 126: 11.201 distance: 98 - 99: 5.343 distance: 99 - 100: 11.801 distance: 99 - 101: 13.505 distance: 102 - 103: 8.707 distance: 103 - 104: 12.375 distance: 103 - 106: 7.474 distance: 104 - 105: 10.005 distance: 104 - 109: 15.374 distance: 105 - 132: 21.694 distance: 106 - 107: 7.348 distance: 106 - 108: 10.968