Starting phenix.real_space_refine on Sun Aug 4 03:55:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scj_25036/08_2024/7scj_25036.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scj_25036/08_2024/7scj_25036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scj_25036/08_2024/7scj_25036.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scj_25036/08_2024/7scj_25036.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scj_25036/08_2024/7scj_25036.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scj_25036/08_2024/7scj_25036.cif" } resolution = 3.4 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= 0.002 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 45 5.16 5 C 5991 2.51 5 N 1562 2.21 5 O 1734 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 9336 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4596 Classifications: {'peptide': 563} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 537} Chain breaks: 3 Chain: "B" Number of atoms: 4596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4596 Classifications: {'peptide': 568} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 34, 'TRANS': 533} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 41 Unusual residues: {'BDP': 1, 'NDG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'UDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'UDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.75, per 1000 atoms: 0.62 Number of scatterers: 9336 At special positions: 0 Unit cell: (98.532, 86.112, 110.124, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 45 16.00 P 4 15.00 O 1734 8.00 N 1562 7.00 C 5991 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 103 " distance=2.03 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 355 " distance=1.99 Simple disulfide: pdb=" SG CYS A 652 " - pdb=" SG CYS A 704 " distance=2.03 Simple disulfide: pdb=" SG CYS B 85 " - pdb=" SG CYS B 90 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 151 " distance=2.02 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 339 " distance=2.03 Simple disulfide: pdb=" SG CYS B 626 " - pdb=" SG CYS B 676 " 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 Links applied ALPHA1-4 " BDP D 2 " - " NDG D 3 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NDG D 1 " - " BDP D 2 " NAG-ASN " NAG A 901 " - " ASN A 330 " " NAG C 1 " - " ASN B 637 " Time building additional restraints: 4.20 Conformation dependent library (CDL) restraints added in 1.6 seconds 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2158 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 14 sheets defined 37.2% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 105 through 111 removed outlier: 3.714A pdb=" N CYS A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LYS A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 141 Processing helix chain 'A' and resid 173 through 180 Processing helix chain 'A' and resid 222 through 226 removed outlier: 3.536A pdb=" N PHE A 226 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 303 through 308 removed outlier: 4.011A pdb=" N HIS A 307 " --> pdb=" O ASP A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 320 removed outlier: 4.326A pdb=" N ASP A 313 " --> pdb=" O ASP A 309 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ARG A 314 " --> pdb=" O SER A 310 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR A 317 " --> pdb=" O ASP A 313 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A 320 " --> pdb=" O ASN A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 330 Processing helix chain 'A' and resid 345 through 353 Processing helix chain 'A' and resid 388 through 396 Processing helix chain 'A' and resid 397 through 416 Processing helix chain 'A' and resid 418 through 432 Processing helix chain 'A' and resid 441 through 446 removed outlier: 3.731A pdb=" N TRP A 445 " --> pdb=" O ASN A 441 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 441 through 446' Processing helix chain 'A' and resid 461 through 465 Processing helix chain 'A' and resid 571 through 585 removed outlier: 3.706A pdb=" N SER A 584 " --> pdb=" O THR A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 639 through 649 removed outlier: 3.917A pdb=" N LYS A 643 " --> pdb=" O PRO A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 666 Processing helix chain 'A' and resid 699 through 713 removed outlier: 3.934A pdb=" N SER A 703 " --> pdb=" O ALA A 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 139 Processing helix chain 'B' and resid 166 through 176 Processing helix chain 'B' and resid 180 through 184 Processing helix chain 'B' and resid 235 through 240 Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 308 through 312 removed outlier: 3.989A pdb=" N LEU B 312 " --> pdb=" O TYR B 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 308 through 312' Processing helix chain 'B' and resid 313 through 315 No H-bonds generated for 'chain 'B' and resid 313 through 315' Processing helix chain 'B' and resid 329 through 338 removed outlier: 3.743A pdb=" N ASP B 333 " --> pdb=" O ALA B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 366 through 370 removed outlier: 3.608A pdb=" N MET B 370 " --> pdb=" O GLU B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 379 Processing helix chain 'B' and resid 381 through 399 Processing helix chain 'B' and resid 402 through 419 Processing helix chain 'B' and resid 420 through 423 Processing helix chain 'B' and resid 425 through 430 Processing helix chain 'B' and resid 432 through 439 Processing helix chain 'B' and resid 467 through 478 removed outlier: 3.765A pdb=" N ARG B 471 " --> pdb=" O GLU B 467 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS B 478 " --> pdb=" O THR B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 523 removed outlier: 3.938A pdb=" N ARG B 522 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE B 523 " --> pdb=" O SER B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 559 removed outlier: 3.704A pdb=" N GLU B 558 " --> pdb=" O GLU B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 610 Processing helix chain 'B' and resid 615 through 624 Processing helix chain 'B' and resid 627 through 640 Processing helix chain 'B' and resid 669 through 685 Processing sheet with id=AA1, first strand: chain 'A' and resid 144 through 145 removed outlier: 6.052A pdb=" N VAL A 116 " --> pdb=" O THR A 145 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N PHE A 154 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N PHE A 193 " --> pdb=" O PHE A 154 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N HIS A 190 " --> pdb=" O MET A 215 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ALA A 217 " --> pdb=" O HIS A 190 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE A 192 " --> pdb=" O ALA A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 162 through 163 removed outlier: 7.161A pdb=" N TYR A 196 " --> pdb=" O ARG A 163 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 292 through 297 removed outlier: 6.386A pdb=" N LEU A 264 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N LEU A 295 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N PHE A 266 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N THR A 297 " --> pdb=" O PHE A 266 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N GLY A 268 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL A 265 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N CYS A 334 " --> pdb=" O VAL A 358 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 510 through 517 removed outlier: 6.575A pdb=" N PHE A 480 " --> pdb=" O CYS A 510 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLN A 512 " --> pdb=" O PHE A 480 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 594 through 595 Processing sheet with id=AA6, first strand: chain 'A' and resid 599 through 600 Processing sheet with id=AA7, first strand: chain 'A' and resid 724 through 726 removed outlier: 6.522A pdb=" N LYS B 645 " --> pdb=" O ALA B 696 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA B 536 " --> pdb=" O ALA B 598 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU B 535 " --> pdb=" O THR B 457 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU B 461 " --> pdb=" O ILE B 537 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE B 456 " --> pdb=" O LYS B 484 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N LEU B 486 " --> pdb=" O PHE B 456 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ALA B 458 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL B 488 " --> pdb=" O ALA B 458 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL B 460 " --> pdb=" O VAL B 488 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS B 510 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 106 through 108 Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 189 removed outlier: 6.598A pdb=" N LEU B 212 " --> pdb=" O VAL B 228 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 217 through 218 removed outlier: 4.749A pdb=" N PHE B 217 " --> pdb=" O ILE B 349 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 254 through 257 removed outlier: 7.161A pdb=" N LEU B 254 " --> pdb=" O LEU B 281 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N LEU B 283 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N SER B 256 " --> pdb=" O LEU B 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 298 through 301 removed outlier: 3.546A pdb=" N GLN B 304 " --> pdb=" O HIS B 301 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 317 through 320 removed outlier: 6.755A pdb=" N CYS B 318 " --> pdb=" O VAL B 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 570 through 574 removed outlier: 3.655A pdb=" N LYS B 579 " --> pdb=" O ASP B 574 " (cutoff:3.500A) 291 hydrogen bonds defined for protein. 825 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.70 Time building geometry restraints manager: 4.50 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: 2933 1.34 - 1.46: 1705 1.46 - 1.58: 4872 1.58 - 1.69: 5 1.69 - 1.81: 70 Bond restraints: 9585 Sorted by residual: bond pdb=" O1A UDP A 902 " pdb=" PA UDP A 902 " ideal model delta sigma weight residual 1.482 1.524 -0.042 1.00e-02 1.00e+04 1.76e+01 bond pdb=" N VAL A 265 " pdb=" CA VAL A 265 " ideal model delta sigma weight residual 1.456 1.492 -0.035 1.14e-02 7.69e+03 9.58e+00 bond pdb=" N GLU B 397 " pdb=" CA GLU B 397 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.35e-02 5.49e+03 7.53e+00 bond pdb=" O3A UDP A 902 " pdb=" PB UDP A 902 " ideal model delta sigma weight residual 1.584 1.611 -0.027 1.00e-02 1.00e+04 7.16e+00 bond pdb=" O2A UDP A 902 " pdb=" PA UDP A 902 " ideal model delta sigma weight residual 1.527 1.481 0.046 1.80e-02 3.09e+03 6.43e+00 ... (remaining 9580 not shown) Histogram of bond angle deviations from ideal: 98.82 - 105.86: 249 105.86 - 112.90: 5102 112.90 - 119.94: 3277 119.94 - 126.98: 4263 126.98 - 134.02: 143 Bond angle restraints: 13034 Sorted by residual: angle pdb=" O3A UDP A 902 " pdb=" PB UDP A 902 " pdb=" O3B UDP A 902 " ideal model delta sigma weight residual 112.01 103.72 8.29 1.00e+00 1.00e+00 6.88e+01 angle pdb=" O5' UDP A 902 " pdb=" PA UDP A 902 " pdb=" O1A UDP A 902 " ideal model delta sigma weight residual 106.70 111.11 -4.41 1.00e+00 1.00e+00 1.95e+01 angle pdb=" O5' UDP A 902 " pdb=" PA UDP A 902 " pdb=" O2A UDP A 902 " ideal model delta sigma weight residual 110.83 106.99 3.84 1.00e+00 1.00e+00 1.47e+01 angle pdb=" C TYR A 262 " pdb=" CA TYR A 262 " pdb=" CB TYR A 262 " ideal model delta sigma weight residual 112.43 105.20 7.23 1.91e+00 2.74e-01 1.43e+01 angle pdb=" C TYR B 399 " pdb=" CA TYR B 399 " pdb=" CB TYR B 399 " ideal model delta sigma weight residual 109.65 115.28 -5.63 1.68e+00 3.54e-01 1.12e+01 ... (remaining 13029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.04: 5571 24.04 - 48.09: 198 48.09 - 72.13: 39 72.13 - 96.17: 21 96.17 - 120.21: 11 Dihedral angle restraints: 5840 sinusoidal: 2500 harmonic: 3340 Sorted by residual: dihedral pdb=" C3 NDG D 3 " pdb=" C4 NDG D 3 " pdb=" C5 NDG D 3 " pdb=" O5 NDG D 3 " ideal model delta sinusoidal sigma weight residual 53.31 -66.90 120.21 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" C3 NDG D 3 " pdb=" C4 NDG D 3 " pdb=" C5 NDG D 3 " pdb=" C6 NDG D 3 " ideal model delta sinusoidal sigma weight residual 287.69 173.81 113.88 1 3.00e+01 1.11e-03 1.50e+01 dihedral pdb=" O4 NDG D 3 " pdb=" C4 NDG D 3 " pdb=" C5 NDG D 3 " pdb=" O5 NDG D 3 " ideal model delta sinusoidal sigma weight residual 286.72 174.60 112.12 1 3.00e+01 1.11e-03 1.47e+01 ... (remaining 5837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 1419 0.129 - 0.257: 10 0.257 - 0.386: 3 0.386 - 0.515: 1 0.515 - 0.643: 1 Chirality restraints: 1434 Sorted by residual: chirality pdb=" C1 BDP D 2 " pdb=" O4 NDG D 1 " pdb=" C2 BDP D 2 " pdb=" O5 BDP D 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-02 2.50e+03 1.03e+03 chirality pdb=" C1 NDG D 3 " pdb=" O4 BDP D 2 " pdb=" C2 NDG D 3 " pdb=" O5 NDG D 3 " both_signs ideal model delta sigma weight residual False 2.40 1.94 0.46 2.00e-02 2.50e+03 5.18e+02 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 3.67e+00 ... (remaining 1431 not shown) Planarity restraints: 1646 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NDG D 3 " 0.183 2.00e-02 2.50e+03 1.57e-01 3.09e+02 pdb=" C7 NDG D 3 " -0.038 2.00e-02 2.50e+03 pdb=" C8 NDG D 3 " -0.029 2.00e-02 2.50e+03 pdb=" N2 NDG D 3 " -0.259 2.00e-02 2.50e+03 pdb=" O7 NDG D 3 " 0.143 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NDG D 1 " 0.073 2.00e-02 2.50e+03 6.12e-02 4.68e+01 pdb=" C7 NDG D 1 " -0.017 2.00e-02 2.50e+03 pdb=" C8 NDG D 1 " 0.054 2.00e-02 2.50e+03 pdb=" N2 NDG D 1 " -0.100 2.00e-02 2.50e+03 pdb=" O7 NDG D 1 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 330 " 0.043 2.00e-02 2.50e+03 4.30e-02 2.31e+01 pdb=" CG ASN A 330 " -0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN A 330 " -0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN A 330 " -0.064 2.00e-02 2.50e+03 pdb=" C1 NAG A 901 " 0.053 2.00e-02 2.50e+03 ... (remaining 1643 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 725 2.74 - 3.28: 9357 3.28 - 3.82: 15558 3.82 - 4.36: 18907 4.36 - 4.90: 32053 Nonbonded interactions: 76600 Sorted by model distance: nonbonded pdb=" OG1 THR A 673 " pdb=" OD1 ASP A 725 " model vdw 2.200 3.040 nonbonded pdb=" OH TYR B 130 " pdb=" O PRO B 155 " model vdw 2.204 3.040 nonbonded pdb=" NZ LYS A 400 " pdb=" O TYR B 421 " model vdw 2.210 3.120 nonbonded pdb=" O GLU B 548 " pdb=" OH TYR B 566 " model vdw 2.231 3.040 nonbonded pdb=" O ASP A 164 " pdb=" OG SER A 167 " model vdw 2.234 3.040 ... (remaining 76595 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 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: 0.690 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: 0.000 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 29.090 Find NCS groups from input model: 0.150 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 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 0.046 9585 Z= 0.241 Angle : 0.602 8.293 13034 Z= 0.324 Chirality : 0.051 0.643 1434 Planarity : 0.006 0.157 1644 Dihedral : 14.792 120.214 3655 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.25), residues: 1113 helix: 0.86 (0.28), residues: 366 sheet: -0.41 (0.51), residues: 110 loop : -0.71 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 711 HIS 0.002 0.001 HIS B 694 PHE 0.012 0.001 PHE B 400 TYR 0.033 0.002 TYR B 399 ARG 0.003 0.000 ARG A 384 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 TYR cc_start: 0.7867 (m-10) cc_final: 0.7593 (m-10) REVERT: A 115 LYS cc_start: 0.7464 (mmmm) cc_final: 0.7214 (mttm) REVERT: A 125 GLU cc_start: 0.6568 (mt-10) cc_final: 0.6169 (mt-10) REVERT: A 225 ASN cc_start: 0.8047 (m110) cc_final: 0.7810 (m110) REVERT: A 261 LYS cc_start: 0.7545 (ttpp) cc_final: 0.7305 (ttpp) REVERT: A 291 ASP cc_start: 0.6458 (p0) cc_final: 0.6249 (p0) REVERT: A 359 MET cc_start: 0.7948 (mpp) cc_final: 0.7498 (mpp) REVERT: A 420 GLU cc_start: 0.7043 (tm-30) cc_final: 0.6669 (tt0) REVERT: A 455 LEU cc_start: 0.7969 (mt) cc_final: 0.7755 (mt) REVERT: A 471 ASN cc_start: 0.6771 (m110) cc_final: 0.6554 (m-40) REVERT: A 715 MET cc_start: 0.6937 (tpp) cc_final: 0.6582 (tpp) REVERT: B 99 ASN cc_start: 0.7745 (p0) cc_final: 0.7448 (p0) REVERT: B 135 MET cc_start: 0.6968 (mmp) cc_final: 0.6692 (mmp) REVERT: B 188 LEU cc_start: 0.7393 (mm) cc_final: 0.7000 (mt) REVERT: B 265 TYR cc_start: 0.7228 (m-80) cc_final: 0.6894 (m-80) REVERT: B 267 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7450 (mm-30) REVERT: B 270 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6948 (mm-30) REVERT: B 333 ASP cc_start: 0.7318 (m-30) cc_final: 0.6931 (m-30) REVERT: B 357 ASP cc_start: 0.7261 (t0) cc_final: 0.6967 (t0) REVERT: B 416 ASP cc_start: 0.7494 (m-30) cc_final: 0.7229 (m-30) REVERT: B 549 LEU cc_start: 0.7901 (mm) cc_final: 0.7584 (mp) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.2501 time to fit residues: 88.4317 Evaluate side-chains 239 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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: 67.5876 > 50: distance: 73 - 74: 11.669 distance: 73 - 76: 3.774 distance: 74 - 75: 13.101 distance: 74 - 80: 9.676 distance: 76 - 77: 5.244 distance: 77 - 78: 13.931 distance: 77 - 79: 4.620 distance: 80 - 81: 8.548 distance: 80 - 174: 4.317 distance: 81 - 82: 31.943 distance: 81 - 84: 10.544 distance: 82 - 83: 12.864 distance: 82 - 87: 27.239 distance: 83 - 185: 29.913 distance: 84 - 85: 11.472 distance: 84 - 86: 6.768 distance: 87 - 88: 17.752 distance: 88 - 89: 24.074 distance: 88 - 91: 17.958 distance: 89 - 90: 29.068 distance: 89 - 94: 15.540 distance: 91 - 92: 18.536 distance: 91 - 93: 23.871 distance: 94 - 95: 11.386 distance: 94 - 188: 27.864 distance: 95 - 96: 25.280 distance: 95 - 98: 13.151 distance: 96 - 97: 26.730 distance: 96 - 108: 35.557 distance: 98 - 99: 15.316 distance: 99 - 100: 8.813 distance: 99 - 101: 3.448 distance: 100 - 102: 7.238 distance: 101 - 103: 8.414 distance: 101 - 104: 3.482 distance: 102 - 103: 3.245 distance: 103 - 105: 7.092 distance: 104 - 106: 5.140 distance: 105 - 107: 3.573 distance: 106 - 107: 7.718 distance: 108 - 109: 4.998 distance: 109 - 110: 3.192 distance: 109 - 112: 7.116 distance: 110 - 111: 26.708 distance: 110 - 116: 13.502 distance: 112 - 113: 4.503 distance: 113 - 114: 5.970 distance: 113 - 115: 5.800 distance: 116 - 117: 8.306 distance: 117 - 118: 7.321 distance: 117 - 120: 3.021 distance: 118 - 119: 19.186 distance: 118 - 124: 4.291 distance: 120 - 121: 12.421 distance: 121 - 122: 6.753 distance: 121 - 123: 4.686 distance: 124 - 125: 6.683 distance: 125 - 126: 8.787 distance: 125 - 128: 12.262 distance: 126 - 127: 29.767 distance: 126 - 133: 8.007 distance: 128 - 129: 10.957 distance: 129 - 130: 7.554 distance: 130 - 131: 6.642 distance: 130 - 132: 8.098 distance: 133 - 134: 17.083 distance: 134 - 135: 25.521 distance: 134 - 137: 13.245 distance: 135 - 136: 17.297 distance: 135 - 141: 38.059 distance: 137 - 138: 13.325 distance: 138 - 139: 14.667 distance: 138 - 140: 11.739 distance: 141 - 142: 48.544 distance: 142 - 143: 25.870 distance: 142 - 145: 16.988 distance: 143 - 144: 12.824 distance: 143 - 150: 12.960 distance: 145 - 146: 20.338 distance: 146 - 147: 9.209 distance: 147 - 148: 9.871 distance: 148 - 149: 6.450 distance: 150 - 151: 17.252 distance: 151 - 152: 24.306 distance: 151 - 154: 45.124 distance: 152 - 153: 19.666 distance: 152 - 158: 18.212 distance: 154 - 155: 12.907 distance: 155 - 156: 42.455 distance: 155 - 157: 36.195