Starting phenix.real_space_refine on Mon Jun 9 15:42:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x2n_38018/06_2025/8x2n_38018.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x2n_38018/06_2025/8x2n_38018.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x2n_38018/06_2025/8x2n_38018.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x2n_38018/06_2025/8x2n_38018.map" model { file = "/net/cci-nas-00/data/ceres_data/8x2n_38018/06_2025/8x2n_38018.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x2n_38018/06_2025/8x2n_38018.cif" } resolution = 3.18 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= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 7085 2.51 5 N 1769 2.21 5 O 1886 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 10775 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5398 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 705, 5387 Classifications: {'peptide': 705} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 673} Chain breaks: 1 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 54 Conformer: "B" Number of residues, atoms: 705, 5387 Classifications: {'peptide': 705} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 673} Chain breaks: 1 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 54 bond proxies already assigned to first conformer: 5492 Chain: "B" Number of atoms: 5377 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 701, 5366 Classifications: {'peptide': 701} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 669} Chain breaks: 1 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 63 Conformer: "B" Number of residues, atoms: 701, 5366 Classifications: {'peptide': 701} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 669} Chain breaks: 1 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 63 bond proxies already assigned to first conformer: 5470 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N APHE A 58 " occ=0.39 ... (20 atoms not shown) pdb=" CZ BPHE A 58 " occ=0.61 residue: pdb=" N APHE B 58 " occ=0.39 ... (20 atoms not shown) pdb=" CZ BPHE B 58 " occ=0.61 Time building chain proxies: 11.33, per 1000 atoms: 1.05 Number of scatterers: 10775 At special positions: 0 Unit cell: (105.664, 112.32, 104, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 35 16.00 O 1886 8.00 N 1769 7.00 C 7085 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: 2.43 Conformation dependent library (CDL) restraints added in 2.6 seconds 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 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: 63 helices and 4 sheets defined 68.5% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 17 through 25 Processing helix chain 'A' and resid 34 through 43 Processing helix chain 'A' and resid 46 through 58 Processing helix chain 'A' and resid 58 through 64 removed outlier: 3.918A pdb=" N SER A 62 " --> pdb=" O APHE A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 98 removed outlier: 3.857A pdb=" N LEU A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LEU A 74 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 120 removed outlier: 4.010A pdb=" N GLY A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) Proline residue: A 112 - end of helix removed outlier: 4.450A pdb=" N PHE A 118 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE A 119 " --> pdb=" O ILE A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 148 Processing helix chain 'A' and resid 169 through 196 Processing helix chain 'A' and resid 199 through 205 removed outlier: 4.099A pdb=" N VAL A 202 " --> pdb=" O GLY A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 231 removed outlier: 4.008A pdb=" N LYS A 227 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N PHE A 228 " --> pdb=" O SER A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 253 removed outlier: 3.542A pdb=" N GLN A 253 " --> pdb=" O SER A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 257 Processing helix chain 'A' and resid 258 through 282 Processing helix chain 'A' and resid 291 through 308 Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 332 through 366 removed outlier: 5.688A pdb=" N GLY A 341 " --> pdb=" O GLN A 337 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ASP A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS A 364 " --> pdb=" O VAL A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 388 Processing helix chain 'A' and resid 396 through 407 Processing helix chain 'A' and resid 411 through 427 removed outlier: 3.601A pdb=" N ALA A 427 " --> pdb=" O ILE A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 453 removed outlier: 3.684A pdb=" N LEU A 440 " --> pdb=" O GLN A 436 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLY A 450 " --> pdb=" O GLY A 446 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N MET A 451 " --> pdb=" O ASN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 465 Processing helix chain 'A' and resid 465 through 482 Processing helix chain 'A' and resid 483 through 503 removed outlier: 3.536A pdb=" N LEU A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA A 489 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR A 503 " --> pdb=" O ILE A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 547 No H-bonds generated for 'chain 'A' and resid 545 through 547' Processing helix chain 'A' and resid 548 through 561 Processing helix chain 'A' and resid 563 through 585 Processing helix chain 'A' and resid 612 through 618 Processing helix chain 'A' and resid 660 through 677 removed outlier: 3.696A pdb=" N GLY A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 677 " --> pdb=" O GLU A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 697 removed outlier: 3.509A pdb=" N ILE A 691 " --> pdb=" O ASP A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 707 No H-bonds generated for 'chain 'A' and resid 705 through 707' Processing helix chain 'A' and resid 712 through 728 Processing helix chain 'B' and resid 17 through 25 Processing helix chain 'B' and resid 34 through 43 Processing helix chain 'B' and resid 46 through 58 Processing helix chain 'B' and resid 58 through 64 removed outlier: 3.927A pdb=" N SER B 62 " --> pdb=" O APHE B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 99 removed outlier: 4.329A pdb=" N SER B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 120 removed outlier: 4.116A pdb=" N TYR B 107 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA B 108 " --> pdb=" O TYR B 104 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER B 109 " --> pdb=" O GLY B 105 " (cutoff:3.500A) Proline residue: B 112 - end of helix removed outlier: 3.696A pdb=" N PHE B 118 " --> pdb=" O ILE B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 148 Processing helix chain 'B' and resid 170 through 196 Processing helix chain 'B' and resid 199 through 205 removed outlier: 4.082A pdb=" N VAL B 202 " --> pdb=" O GLY B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 230 removed outlier: 3.757A pdb=" N LYS B 227 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE B 228 " --> pdb=" O SER B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 253 removed outlier: 3.697A pdb=" N LYS B 245 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL B 246 " --> pdb=" O SER B 242 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN B 253 " --> pdb=" O SER B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 282 Processing helix chain 'B' and resid 291 through 308 Processing helix chain 'B' and resid 308 through 314 Processing helix chain 'B' and resid 332 through 339 Processing helix chain 'B' and resid 339 through 366 removed outlier: 3.520A pdb=" N LYS B 364 " --> pdb=" O VAL B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 388 removed outlier: 3.501A pdb=" N PHE B 388 " --> pdb=" O VAL B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 407 Processing helix chain 'B' and resid 411 through 427 Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 436 through 448 removed outlier: 3.535A pdb=" N LEU B 440 " --> pdb=" O GLN B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 453 Processing helix chain 'B' and resid 455 through 465 removed outlier: 4.449A pdb=" N GLY B 459 " --> pdb=" O PHE B 455 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG B 463 " --> pdb=" O GLY B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 482 Processing helix chain 'B' and resid 483 through 503 removed outlier: 3.538A pdb=" N ALA B 489 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR B 503 " --> pdb=" O ILE B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 561 removed outlier: 4.807A pdb=" N GLY B 550 " --> pdb=" O PHE B 546 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N PHE B 551 " --> pdb=" O ALA B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 585 Processing helix chain 'B' and resid 610 through 618 removed outlier: 3.584A pdb=" N ILE B 613 " --> pdb=" O ASN B 610 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLU B 614 " --> pdb=" O ASN B 611 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN B 618 " --> pdb=" O VAL B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 677 Processing helix chain 'B' and resid 687 through 697 Processing helix chain 'B' and resid 705 through 707 No H-bonds generated for 'chain 'B' and resid 705 through 707' Processing helix chain 'B' and resid 712 through 725 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 14 Processing sheet with id=AA2, first strand: chain 'A' and resid 520 through 522 removed outlier: 4.502A pdb=" N ILE A 537 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N ASN A 513 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 12.051A pdb=" N VAL A 535 " --> pdb=" O ASN A 513 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N PHE A 710 " --> pdb=" O VAL A 681 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ILE A 683 " --> pdb=" O PHE A 710 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 520 through 522 removed outlier: 4.359A pdb=" N ILE B 537 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ASN B 513 " --> pdb=" O VAL B 535 " (cutoff:3.500A) removed outlier: 12.160A pdb=" N VAL B 535 " --> pdb=" O ASN B 513 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LYS B 536 " --> pdb=" O ILE B 650 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ASP B 652 " --> pdb=" O LYS B 536 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N PHE B 538 " --> pdb=" O ASP B 652 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N PHE B 710 " --> pdb=" O VAL B 681 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE B 683 " --> pdb=" O PHE B 710 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 587 through 588 696 hydrogen bonds defined for protein. 2025 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: 3.12 Time building geometry restraints manager: 2.93 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: 3370 1.34 - 1.46: 2383 1.46 - 1.58: 5209 1.58 - 1.70: 0 1.70 - 1.82: 52 Bond restraints: 11014 Sorted by residual: bond pdb=" CB PRO B 47 " pdb=" CG PRO B 47 " ideal model delta sigma weight residual 1.492 1.577 -0.085 5.00e-02 4.00e+02 2.87e+00 bond pdb=" C LEU B 64 " pdb=" N PRO B 65 " ideal model delta sigma weight residual 1.335 1.353 -0.019 1.19e-02 7.06e+03 2.44e+00 bond pdb=" CG PRO B 47 " pdb=" CD PRO B 47 " ideal model delta sigma weight residual 1.503 1.456 0.047 3.40e-02 8.65e+02 1.92e+00 bond pdb=" C PHE A 111 " pdb=" N PRO A 112 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.36e-02 5.41e+03 1.76e+00 bond pdb=" C PHE B 130 " pdb=" N PRO B 131 " ideal model delta sigma weight residual 1.335 1.352 -0.016 1.36e-02 5.41e+03 1.42e+00 ... (remaining 11009 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 14632 1.73 - 3.47: 304 3.47 - 5.20: 29 5.20 - 6.93: 15 6.93 - 8.67: 5 Bond angle restraints: 14985 Sorted by residual: angle pdb=" N ASP B 525 " pdb=" CA ASP B 525 " pdb=" C ASP B 525 " ideal model delta sigma weight residual 111.82 119.49 -7.67 1.16e+00 7.43e-01 4.38e+01 angle pdb=" C GLN B 618 " pdb=" N PRO B 619 " pdb=" CA PRO B 619 " ideal model delta sigma weight residual 119.84 126.28 -6.44 1.25e+00 6.40e-01 2.65e+01 angle pdb=" N ASN A 548 " pdb=" CA ASN A 548 " pdb=" C ASN A 548 " ideal model delta sigma weight residual 111.87 118.31 -6.44 1.41e+00 5.03e-01 2.09e+01 angle pdb=" CA PRO B 47 " pdb=" N PRO B 47 " pdb=" CD PRO B 47 " ideal model delta sigma weight residual 112.00 105.87 6.13 1.40e+00 5.10e-01 1.91e+01 angle pdb=" N ILE A 544 " pdb=" CA ILE A 544 " pdb=" C ILE A 544 " ideal model delta sigma weight residual 107.51 113.44 -5.93 1.49e+00 4.50e-01 1.58e+01 ... (remaining 14980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 5977 17.97 - 35.93: 458 35.93 - 53.90: 78 53.90 - 71.86: 13 71.86 - 89.83: 3 Dihedral angle restraints: 6529 sinusoidal: 2447 harmonic: 4082 Sorted by residual: dihedral pdb=" CA MET A 296 " pdb=" C MET A 296 " pdb=" N THR A 297 " pdb=" CA THR A 297 " ideal model delta harmonic sigma weight residual 180.00 162.11 17.89 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA TYR A 16 " pdb=" C TYR A 16 " pdb=" N SER A 17 " pdb=" CA SER A 17 " ideal model delta harmonic sigma weight residual 180.00 162.20 17.80 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA PHE A 110 " pdb=" C PHE A 110 " pdb=" N PHE A 111 " pdb=" CA PHE A 111 " ideal model delta harmonic sigma weight residual 180.00 -163.15 -16.85 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 6526 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1515 0.057 - 0.114: 248 0.114 - 0.171: 29 0.171 - 0.228: 3 0.228 - 0.285: 2 Chirality restraints: 1797 Sorted by residual: chirality pdb=" CA ASN A 548 " pdb=" N ASN A 548 " pdb=" C ASN A 548 " pdb=" CB ASN A 548 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA ASP B 525 " pdb=" N ASP B 525 " pdb=" C ASP B 525 " pdb=" CB ASP B 525 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA TYR A 204 " pdb=" N TYR A 204 " pdb=" C TYR A 204 " pdb=" CB TYR A 204 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1794 not shown) Planarity restraints: 1875 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 46 " -0.039 5.00e-02 4.00e+02 5.70e-02 5.20e+00 pdb=" N PRO B 47 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 47 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 47 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 524 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.71e+00 pdb=" C LYS B 524 " -0.038 2.00e-02 2.50e+03 pdb=" O LYS B 524 " 0.014 2.00e-02 2.50e+03 pdb=" N ASP B 525 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 590 " 0.031 5.00e-02 4.00e+02 4.71e-02 3.55e+00 pdb=" N PRO B 591 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 591 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 591 " 0.026 5.00e-02 4.00e+02 ... (remaining 1872 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1324 2.75 - 3.29: 11227 3.29 - 3.82: 18052 3.82 - 4.36: 20560 4.36 - 4.90: 36325 Nonbonded interactions: 87488 Sorted by model distance: nonbonded pdb=" OD1 ASP B 701 " pdb=" N GLY B 702 " model vdw 2.209 3.120 nonbonded pdb=" O ILE A 544 " pdb=" OG SER A 663 " model vdw 2.228 3.040 nonbonded pdb=" OG1 THR B 503 " pdb=" OH TYR B 545 " model vdw 2.243 3.040 nonbonded pdb=" OE1 GLU A 207 " pdb=" NH1 ARG B 665 " model vdw 2.250 3.120 nonbonded pdb=" OG SER B 75 " pdb=" O GLY B 407 " model vdw 2.275 3.040 ... (remaining 87483 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 23 or (resid 24 and (name N or name CA or name C \ or name O or name CB )) or resid 25 through 37 or (resid 38 and (name N or name \ CA or name C or name O or name CB )) or resid 39 through 57 or resid 59 through \ 70 or (resid 71 and (name N or name CA or name C or name O or name CB )) or res \ id 72 through 168 or resid 170 through 206 or (resid 207 and (name N or name CA \ or name C or name O or name CB )) or resid 208 through 260 or (resid 261 and (na \ me N or name CA or name C or name O or name CB )) or resid 262 through 295 or (r \ esid 296 and (name N or name CA or name C or name O or name CB )) or resid 297 t \ hrough 347 or (resid 348 and (name N or name CA or name C or name O or name CB ) \ ) or resid 349 through 393 or (resid 394 and (name N or name CA or name C or nam \ e O or name CB )) or resid 395 through 605 or (resid 606 and (name N or name CA \ or name C or name O or name CB )) or resid 607 through 686 or (resid 687 through \ 689 and (name N or name CA or name C or name O or name CB )) or resid 690 throu \ gh 724 or (resid 725 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'B' and (resid 7 through 25 or (resid 26 and (name N or name CA or name C \ or name O or name CB )) or resid 27 through 50 or (resid 51 and (name N or name \ CA or name C or name O or name CB )) or resid 52 through 57 or resid 59 through \ 66 or (resid 67 through 68 and (name N or name CA or name C or name O or name C \ B )) or resid 69 through 74 or (resid 75 through 76 and (name N or name CA or na \ me C or name O or name CB )) or resid 77 through 78 or (resid 79 and (name N or \ name CA or name C or name O or name CB )) or resid 80 through 280 or (resid 281 \ and (name N or name CA or name C or name O or name CB )) or resid 282 through 40 \ 5 or (resid 406 and (name N or name CA or name C or name O or name CB )) or resi \ d 407 through 422 or (resid 423 and (name N or name CA or name C or name O or na \ me CB )) or resid 424 through 464 or (resid 465 and (name N or name CA or name C \ or name O or name CB )) or resid 466 through 586 or (resid 587 through 590 and \ (name N or name CA or name C or name O or name CB )) or resid 591 through 604 or \ (resid 605 through 606 and (name N or name CA or name C or name O or name CB )) \ or resid 607 through 636 or (resid 637 and (name N or name CA or name C or name \ O or name CB )) or resid 638 through 721 or (resid 722 and (name N or name CA o \ r name C or name O or name CB )) or resid 723 through 725)) } 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=0.39 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 32.580 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.070 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: 38.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 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 0.085 11014 Z= 0.170 Angle : 0.626 8.667 14985 Z= 0.365 Chirality : 0.043 0.285 1797 Planarity : 0.004 0.057 1875 Dihedral : 13.225 89.827 3893 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.26 % Allowed : 15.52 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.52 (0.22), residues: 1404 helix: 1.59 (0.17), residues: 903 sheet: 2.19 (1.01), residues: 36 loop : -0.16 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 472 HIS 0.004 0.001 HIS A 237 PHE 0.021 0.001 PHE A 94 TYR 0.021 0.002 TYR A 367 ARG 0.008 0.000 ARG B 579 Details of bonding type rmsd hydrogen bonds : bond 0.13762 ( 696) hydrogen bonds : angle 5.62289 ( 2025) covalent geometry : bond 0.00362 (11014) covalent geometry : angle 0.62571 (14985) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 118 time to evaluate : 1.220 Fit side-chains REVERT: A 397 LEU cc_start: 0.7650 (tp) cc_final: 0.7408 (tp) REVERT: B 276 LYS cc_start: 0.7432 (tttt) cc_final: 0.7204 (ttmt) outliers start: 3 outliers final: 1 residues processed: 119 average time/residue: 0.2236 time to fit residues: 39.1462 Evaluate side-chains 111 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 545 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 58 optimal weight: 0.0010 chunk 36 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 109 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 127 optimal weight: 50.0000 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 ASN A 513 ASN B 90 GLN B 124 HIS ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.150789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.119317 restraints weight = 32752.153| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 3.13 r_work: 0.3157 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3143 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.0738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11014 Z= 0.166 Angle : 0.558 6.454 14985 Z= 0.296 Chirality : 0.042 0.169 1797 Planarity : 0.004 0.044 1875 Dihedral : 3.883 20.832 1498 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.18 % Allowed : 13.25 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.71 (0.22), residues: 1404 helix: 1.73 (0.17), residues: 907 sheet: 2.76 (0.98), residues: 36 loop : -0.13 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 63 HIS 0.003 0.001 HIS A 237 PHE 0.020 0.002 PHE A 94 TYR 0.016 0.002 TYR A 9 ARG 0.007 0.001 ARG B 579 Details of bonding type rmsd hydrogen bonds : bond 0.04935 ( 696) hydrogen bonds : angle 4.62259 ( 2025) covalent geometry : bond 0.00383 (11014) covalent geometry : angle 0.55829 (14985) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 1.131 Fit side-chains revert: symmetry clash REVERT: A 397 LEU cc_start: 0.7549 (tp) cc_final: 0.7263 (tp) REVERT: B 276 LYS cc_start: 0.7812 (tttt) cc_final: 0.7364 (ttmt) REVERT: B 692 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7781 (tp30) outliers start: 25 outliers final: 13 residues processed: 141 average time/residue: 0.2031 time to fit residues: 42.7679 Evaluate side-chains 126 residues out of total 1210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 692 GLU Chi-restraints excluded: chain B residue 712 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.4535 > 50: distance: 5 - 26: 10.953 distance: 10 - 34: 12.424 distance: 10 - 45: 10.182 distance: 21 - 22: 21.850 distance: 21 - 24: 24.464 distance: 22 - 23: 7.914 distance: 22 - 26: 9.371 distance: 24 - 25: 9.218 distance: 26 - 27: 7.067 distance: 27 - 28: 11.870 distance: 27 - 30: 14.041 distance: 28 - 29: 7.641 distance: 28 - 34: 5.648 distance: 28 - 45: 5.313 distance: 30 - 31: 5.603 distance: 31 - 32: 14.494 distance: 31 - 33: 9.516 distance: 34 - 35: 4.562 distance: 35 - 36: 6.887 distance: 36 - 37: 9.999 distance: 36 - 56: 5.700 distance: 38 - 39: 4.548 distance: 39 - 40: 7.109 distance: 41 - 43: 5.357 distance: 42 - 44: 3.657 distance: 43 - 44: 7.485 distance: 45 - 46: 8.674 distance: 46 - 49: 12.325 distance: 47 - 48: 4.710 distance: 47 - 56: 5.795 distance: 49 - 50: 7.125 distance: 50 - 51: 10.526 distance: 50 - 52: 11.477 distance: 51 - 53: 5.836 distance: 52 - 54: 7.895 distance: 53 - 55: 10.334 distance: 54 - 55: 11.556 distance: 56 - 57: 7.363 distance: 56 - 62: 16.334 distance: 57 - 60: 6.692 distance: 58 - 59: 8.885 distance: 58 - 63: 3.468 distance: 59 - 82: 12.190 distance: 60 - 61: 10.330 distance: 61 - 62: 18.925 distance: 63 - 64: 6.070 distance: 64 - 65: 7.414 distance: 64 - 67: 4.093 distance: 65 - 71: 3.470 distance: 66 - 96: 14.292 distance: 67 - 68: 8.044 distance: 67 - 69: 3.405 distance: 68 - 70: 10.972 distance: 71 - 72: 7.147 distance: 72 - 73: 5.215 distance: 72 - 75: 6.625 distance: 73 - 74: 4.876 distance: 73 - 76: 3.059 distance: 76 - 77: 3.716 distance: 77 - 78: 8.771 distance: 77 - 80: 9.997 distance: 78 - 79: 4.571 distance: 80 - 81: 4.846 distance: 82 - 83: 4.640 distance: 83 - 84: 8.341 distance: 84 - 85: 3.993 distance: 86 - 87: 4.639 distance: 87 - 89: 4.472 distance: 89 - 92: 4.404 distance: 90 - 91: 3.433 distance: 92 - 94: 3.690 distance: 93 - 95: 3.846 distance: 94 - 95: 3.132 distance: 97 - 98: 5.275 distance: 97 - 100: 4.934 distance: 98 - 99: 6.844 distance: 100 - 101: 5.073 distance: 101 - 102: 10.797 distance: 101 - 103: 15.180 distance: 104 - 110: 8.992 distance: 105 - 108: 4.481 distance: 106 - 107: 8.407 distance: 106 - 111: 4.674 distance: 108 - 109: 9.238 distance: 109 - 110: 6.050