Starting phenix.real_space_refine on Thu Jan 18 19:57:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scj_25036/01_2024/7scj_25036_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scj_25036/01_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_25036/01_2024/7scj_25036.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scj_25036/01_2024/7scj_25036.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scj_25036/01_2024/7scj_25036_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7scj_25036/01_2024/7scj_25036_updated.pdb" } 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-1.21-5211/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: 5.79, 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: 4.09 Conformation dependent library (CDL) restraints added in 1.7 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... running ksdssp... Secondary structure from input PDB file: 41 helices and 12 sheets defined 31.1% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 106 through 110 Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 174 through 179 Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 278 through 283 removed outlier: 3.634A pdb=" N LEU A 283 " --> pdb=" O THR A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 319 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) Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 389 through 395 Processing helix chain 'A' and resid 398 through 415 Processing helix chain 'A' and resid 419 through 433 removed outlier: 3.919A pdb=" N ARG A 433 " --> pdb=" O ILE A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 445 No H-bonds generated for 'chain 'A' and resid 442 through 445' Processing helix chain 'A' and resid 462 through 464 No H-bonds generated for 'chain 'A' and resid 462 through 464' Processing helix chain 'A' and resid 572 through 584 removed outlier: 3.706A pdb=" N SER A 584 " --> pdb=" O THR A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 623 No H-bonds generated for 'chain 'A' and resid 621 through 623' Processing helix chain 'A' and resid 628 through 636 Processing helix chain 'A' and resid 640 through 648 Processing helix chain 'A' and resid 653 through 665 Processing helix chain 'A' and resid 700 through 712 Processing helix chain 'B' and resid 128 through 138 Processing helix chain 'B' and resid 167 through 177 Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 235 through 239 removed outlier: 3.573A pdb=" N GLU B 239 " --> pdb=" O LEU B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 275 Processing helix chain 'B' and resid 308 through 314 removed outlier: 3.989A pdb=" N LEU B 312 " --> pdb=" O TYR B 308 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLN B 313 " --> pdb=" O PRO B 309 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU B 314 " --> pdb=" O GLN B 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 308 through 314' Processing helix chain 'B' and resid 329 through 337 Processing helix chain 'B' and resid 358 through 360 No H-bonds generated for 'chain 'B' and resid 358 through 360' Processing helix chain 'B' and resid 367 through 370 removed outlier: 3.608A pdb=" N MET B 370 " --> pdb=" O GLU B 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 367 through 370' Processing helix chain 'B' and resid 373 through 379 Processing helix chain 'B' and resid 382 through 398 Processing helix chain 'B' and resid 403 through 418 Processing helix chain 'B' and resid 420 through 422 No H-bonds generated for 'chain 'B' and resid 420 through 422' Processing helix chain 'B' and resid 426 through 429 No H-bonds generated for 'chain 'B' and resid 426 through 429' Processing helix chain 'B' and resid 433 through 438 Processing helix chain 'B' and resid 468 through 477 Processing helix chain 'B' and resid 519 through 522 removed outlier: 3.938A pdb=" N ARG B 522 " --> pdb=" O LEU B 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 519 through 522' Processing helix chain 'B' and resid 546 through 558 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 609 Processing helix chain 'B' and resid 616 through 623 Processing helix chain 'B' and resid 628 through 639 Processing helix chain 'B' and resid 669 through 684 Processing sheet with id= A, first strand: chain 'A' and resid 116 through 118 removed outlier: 6.634A pdb=" N LEU A 153 " --> pdb=" O TYR A 117 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 191 through 193 removed outlier: 6.670A pdb=" N MET A 215 " --> pdb=" O ILE A 192 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 264 through 269 removed outlier: 3.504A pdb=" N PHE A 266 " --> pdb=" O VAL A 293 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 333 through 336 removed outlier: 6.112A pdb=" N VAL A 356 " --> pdb=" O CYS A 334 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL A 336 " --> pdb=" O VAL A 356 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL A 358 " --> pdb=" O VAL A 336 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 623 through 627 removed outlier: 7.431A pdb=" N ALA A 482 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ILE A 513 " --> pdb=" O ALA A 482 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE A 484 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N VAL A 515 " --> pdb=" O ILE A 484 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA A 486 " --> pdb=" O VAL A 515 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TRP A 517 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 106 through 108 removed outlier: 6.345A pdb=" N LEU B 152 " --> pdb=" O TYR B 107 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 187 through 189 removed outlier: 6.575A pdb=" N LEU B 211 " --> pdb=" O LEU B 188 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 254 through 257 Processing sheet with id= I, 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= J, first strand: chain 'B' and resid 317 through 320 removed outlier: 5.779A pdb=" N VAL B 340 " --> pdb=" O CYS B 318 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL B 320 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N VAL B 342 " --> pdb=" O VAL B 320 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 598 through 601 removed outlier: 3.662A pdb=" N ALA B 536 " --> pdb=" O ALA B 598 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR B 457 " --> pdb=" O LEU B 535 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE B 537 " --> pdb=" O THR B 457 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ILE B 459 " --> pdb=" O ILE B 537 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ALA B 458 " --> pdb=" O SER B 483 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LEU B 485 " --> pdb=" O ALA B 458 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL B 460 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N VAL B 487 " --> pdb=" O VAL B 460 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N THR B 462 " --> pdb=" O VAL B 487 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N TRP B 489 " --> pdb=" O THR B 462 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N VAL B 487 " --> pdb=" O PRO B 508 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LYS B 510 " --> pdb=" O VAL B 487 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N TRP B 489 " --> pdb=" O LYS B 510 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL B 512 " --> pdb=" O TRP B 489 " (cutoff:3.500A) Processing sheet with id= L, 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) 217 hydrogen bonds defined for protein. 624 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: 2.56 Time building geometry restraints manager: 4.27 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: 5532 24.04 - 48.09: 193 48.09 - 72.13: 20 72.13 - 96.17: 20 96.17 - 120.21: 11 Dihedral angle restraints: 5776 sinusoidal: 2436 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 5773 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: 737 2.74 - 3.28: 9414 3.28 - 3.82: 15647 3.82 - 4.36: 19030 4.36 - 4.90: 32068 Nonbonded interactions: 76896 Sorted by model distance: nonbonded pdb=" OG1 THR A 673 " pdb=" OD1 ASP A 725 " model vdw 2.200 2.440 nonbonded pdb=" OH TYR B 130 " pdb=" O PRO B 155 " model vdw 2.204 2.440 nonbonded pdb=" NZ LYS A 400 " pdb=" O TYR B 421 " model vdw 2.210 2.520 nonbonded pdb=" O GLU B 548 " pdb=" OH TYR B 566 " model vdw 2.231 2.440 nonbonded pdb=" O ASP A 164 " pdb=" OG SER A 167 " model vdw 2.234 2.440 ... (remaining 76891 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 3.840 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 28.250 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.180 ------------------------------------------------------------------------------- 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= 0.249 Angle : 0.602 8.293 13034 Z= 0.324 Chirality : 0.051 0.643 1434 Planarity : 0.006 0.157 1644 Dihedral : 14.180 120.214 3591 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 : 1.105 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: 0.2547 time to fit residues: 89.8903 Evaluate side-chains 239 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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-1.21-5211/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-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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: 67.5973 > 50: distance: 67 - 72: 11.058 distance: 72 - 73: 15.229 distance: 73 - 74: 17.290 distance: 73 - 76: 13.125 distance: 74 - 75: 18.280 distance: 74 - 80: 17.570 distance: 76 - 77: 7.504 distance: 77 - 78: 26.416 distance: 77 - 79: 9.630 distance: 80 - 81: 36.777 distance: 81 - 82: 46.103 distance: 81 - 84: 43.593 distance: 82 - 83: 16.411 distance: 82 - 87: 25.651 distance: 84 - 85: 29.726 distance: 84 - 86: 32.048 distance: 87 - 88: 49.743 distance: 88 - 89: 17.783 distance: 88 - 91: 47.813 distance: 89 - 90: 35.020 distance: 89 - 94: 24.734 distance: 91 - 92: 29.052 distance: 91 - 93: 32.159 distance: 94 - 95: 3.475 distance: 95 - 96: 42.427 distance: 95 - 98: 37.578 distance: 96 - 97: 25.499 distance: 96 - 108: 40.140 distance: 98 - 99: 31.695 distance: 99 - 100: 21.354 distance: 99 - 101: 16.171 distance: 100 - 102: 13.843 distance: 101 - 103: 18.307 distance: 101 - 104: 4.217 distance: 102 - 103: 16.537 distance: 103 - 105: 9.935 distance: 104 - 106: 10.310 distance: 105 - 107: 5.663 distance: 106 - 107: 13.582 distance: 108 - 109: 23.374 distance: 109 - 110: 12.409 distance: 109 - 112: 8.730 distance: 110 - 111: 40.101 distance: 110 - 116: 26.174 distance: 112 - 113: 16.677 distance: 113 - 114: 12.728 distance: 113 - 115: 10.915 distance: 116 - 117: 12.429 distance: 117 - 118: 7.735 distance: 117 - 120: 7.115 distance: 118 - 119: 29.861 distance: 118 - 124: 16.443 distance: 120 - 121: 26.854 distance: 121 - 122: 10.484 distance: 121 - 123: 11.341 distance: 124 - 125: 7.176 distance: 125 - 126: 27.294 distance: 125 - 128: 30.792 distance: 126 - 127: 50.941 distance: 126 - 133: 6.214 distance: 128 - 129: 25.500 distance: 129 - 130: 13.272 distance: 130 - 131: 12.097 distance: 130 - 132: 14.120 distance: 133 - 134: 24.714 distance: 134 - 135: 41.948 distance: 134 - 137: 23.850 distance: 135 - 136: 15.823 distance: 135 - 141: 24.873 distance: 137 - 138: 31.984 distance: 138 - 139: 30.245 distance: 138 - 140: 24.596 distance: 141 - 142: 56.499 distance: 142 - 143: 33.704 distance: 142 - 145: 17.152 distance: 143 - 144: 9.515 distance: 143 - 150: 18.005 distance: 145 - 146: 36.862 distance: 146 - 147: 11.249 distance: 147 - 148: 11.913 distance: 148 - 149: 8.310 distance: 150 - 151: 14.906 distance: 151 - 152: 33.160 distance: 151 - 154: 43.488 distance: 152 - 153: 33.202 distance: 152 - 158: 24.438 distance: 154 - 155: 26.554 distance: 155 - 156: 47.857 distance: 155 - 157: 40.811