Starting phenix.real_space_refine on Sat Aug 23 11:04:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wh7_37532/08_2025/8wh7_37532.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wh7_37532/08_2025/8wh7_37532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wh7_37532/08_2025/8wh7_37532.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wh7_37532/08_2025/8wh7_37532.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wh7_37532/08_2025/8wh7_37532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wh7_37532/08_2025/8wh7_37532.map" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.306 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 54 5.16 5 C 7194 2.51 5 N 1926 2.21 5 O 2349 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11523 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3685 Classifications: {'peptide': 479} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 463} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3685 Classifications: {'peptide': 479} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 463} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3685 Classifications: {'peptide': 479} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 463} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.32, per 1000 atoms: 0.20 Number of scatterers: 11523 At special positions: 0 Unit cell: (93.74, 98.04, 145.34, 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 54 16.00 O 2349 8.00 N 1926 7.00 C 7194 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 26 " - pdb=" SG CYS A 484 " distance=2.03 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 87 " distance=2.03 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A 491 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 484 " distance=2.03 Simple disulfide: pdb=" SG CYS B 75 " - pdb=" SG CYS B 87 " distance=2.03 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 278 " distance=2.03 Simple disulfide: pdb=" SG CYS B 298 " - pdb=" SG CYS B 323 " distance=2.03 Simple disulfide: pdb=" SG CYS B 491 " - pdb=" SG CYS B 495 " distance=2.03 Simple disulfide: pdb=" SG CYS C 26 " - pdb=" SG CYS C 484 " distance=2.03 Simple disulfide: pdb=" SG CYS C 75 " - pdb=" SG CYS C 87 " distance=2.03 Simple disulfide: pdb=" SG CYS C 179 " - pdb=" SG CYS C 278 " distance=2.03 Simple disulfide: pdb=" SG CYS C 298 " - pdb=" SG CYS C 323 " distance=2.03 Simple disulfide: pdb=" SG CYS C 491 " - pdb=" SG CYS C 495 " distance=2.03 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 Links applied BETA1-2 " BMA D 5 " - " BMA D 6 " " BMA F 5 " - " BMA F 6 " " BMA H 5 " - " BMA H 6 " BETA1-3 " BMA D 4 " - " BMA D 5 " " BMA F 4 " - " BMA F 5 " " BMA H 4 " - " BMA H 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " BETA1-6 " BMA D 3 " - " BMA D 4 " " BMA F 3 " - " BMA F 4 " " BMA H 3 " - " BMA H 4 " NAG-ASN " NAG A 601 " - " ASN A 35 " " NAG A 602 " - " ASN A 105 " " NAG A 603 " - " ASN A 203 " " NAG A 604 " - " ASN A 486 " " NAG B 601 " - " ASN B 35 " " NAG B 602 " - " ASN B 105 " " NAG B 603 " - " ASN B 203 " " NAG B 604 " - " ASN B 486 " " NAG C 601 " - " ASN C 35 " " NAG C 602 " - " ASN C 105 " " NAG C 603 " - " ASN C 203 " " NAG C 604 " - " ASN C 486 " " NAG D 1 " - " ASN A 124 " " NAG E 1 " - " ASN A 307 " " NAG F 1 " - " ASN B 124 " " NAG G 1 " - " ASN B 307 " " NAG H 1 " - " ASN C 124 " " NAG I 1 " - " ASN C 307 " Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 375.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2598 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 31 sheets defined 32.7% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 76 through 82 removed outlier: 3.507A pdb=" N HIS A 80 " --> pdb=" O GLY A 76 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N HIS A 81 " --> pdb=" O ILE A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 92 removed outlier: 3.639A pdb=" N LEU A 92 " --> pdb=" O PHE A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 127 removed outlier: 4.279A pdb=" N ILE A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TRP A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 145 removed outlier: 3.734A pdb=" N LEU A 140 " --> pdb=" O PHE A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 154 removed outlier: 4.025A pdb=" N GLY A 153 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA A 154 " --> pdb=" O SER A 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 150 through 154' Processing helix chain 'A' and resid 192 through 201 Processing helix chain 'A' and resid 229 through 237 Processing helix chain 'A' and resid 385 through 415 removed outlier: 3.805A pdb=" N ILE A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR A 396 " --> pdb=" O VAL A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 428 removed outlier: 3.595A pdb=" N LEU A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 474 removed outlier: 3.723A pdb=" N GLU A 437 " --> pdb=" O ASP A 433 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU A 441 " --> pdb=" O GLU A 437 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE A 442 " --> pdb=" O THR A 438 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE A 443 " --> pdb=" O PHE A 439 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG A 444 " --> pdb=" O THR A 440 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE A 448 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS A 465 " --> pdb=" O ILE A 461 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS A 466 " --> pdb=" O GLY A 462 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU A 467 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A 468 " --> pdb=" O LYS A 464 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 469 " --> pdb=" O LYS A 465 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 472 " --> pdb=" O GLU A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 502 removed outlier: 3.831A pdb=" N ILE A 499 " --> pdb=" O CYS A 495 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER A 500 " --> pdb=" O VAL A 496 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG A 501 " --> pdb=" O ASN A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 510 removed outlier: 3.882A pdb=" N ILE A 510 " --> pdb=" O GLU A 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 82 removed outlier: 3.923A pdb=" N HIS B 81 " --> pdb=" O ILE B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 92 removed outlier: 3.639A pdb=" N LEU B 92 " --> pdb=" O PHE B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 127 removed outlier: 4.286A pdb=" N ILE B 125 " --> pdb=" O SER B 121 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N TRP B 127 " --> pdb=" O MET B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 145 removed outlier: 3.735A pdb=" N LEU B 140 " --> pdb=" O PHE B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 154 removed outlier: 4.024A pdb=" N GLY B 153 " --> pdb=" O THR B 150 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA B 154 " --> pdb=" O SER B 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 150 through 154' Processing helix chain 'B' and resid 192 through 201 Processing helix chain 'B' and resid 229 through 237 Processing helix chain 'B' and resid 385 through 415 removed outlier: 3.796A pdb=" N ILE B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR B 396 " --> pdb=" O VAL B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 428 removed outlier: 3.604A pdb=" N LEU B 427 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY B 428 " --> pdb=" O LEU B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 474 removed outlier: 3.721A pdb=" N GLU B 437 " --> pdb=" O ASP B 433 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU B 441 " --> pdb=" O GLU B 437 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE B 442 " --> pdb=" O THR B 438 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE B 443 " --> pdb=" O PHE B 439 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG B 444 " --> pdb=" O THR B 440 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE B 448 " --> pdb=" O ARG B 444 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU B 449 " --> pdb=" O LEU B 445 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS B 464 " --> pdb=" O ALA B 460 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS B 465 " --> pdb=" O ILE B 461 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS B 466 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU B 467 " --> pdb=" O SER B 463 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL B 469 " --> pdb=" O LYS B 465 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS B 470 " --> pdb=" O LYS B 466 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B 472 " --> pdb=" O GLU B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 502 removed outlier: 3.839A pdb=" N ILE B 499 " --> pdb=" O CYS B 495 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER B 500 " --> pdb=" O VAL B 496 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG B 501 " --> pdb=" O ASN B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 510 removed outlier: 3.894A pdb=" N ILE B 510 " --> pdb=" O GLU B 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 82 removed outlier: 3.916A pdb=" N HIS C 81 " --> pdb=" O ILE C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 92 removed outlier: 3.630A pdb=" N LEU C 92 " --> pdb=" O PHE C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 127 removed outlier: 4.313A pdb=" N ILE C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N TRP C 127 " --> pdb=" O MET C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 145 removed outlier: 3.728A pdb=" N LEU C 140 " --> pdb=" O PHE C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 154 removed outlier: 4.034A pdb=" N GLY C 153 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA C 154 " --> pdb=" O SER C 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 150 through 154' Processing helix chain 'C' and resid 192 through 201 Processing helix chain 'C' and resid 229 through 237 Processing helix chain 'C' and resid 385 through 415 removed outlier: 3.793A pdb=" N ILE C 395 " --> pdb=" O ALA C 391 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR C 396 " --> pdb=" O VAL C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 428 removed outlier: 3.588A pdb=" N LEU C 427 " --> pdb=" O LEU C 423 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY C 428 " --> pdb=" O LEU C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 474 removed outlier: 3.718A pdb=" N GLU C 437 " --> pdb=" O ASP C 433 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU C 441 " --> pdb=" O GLU C 437 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHE C 442 " --> pdb=" O THR C 438 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE C 443 " --> pdb=" O PHE C 439 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG C 444 " --> pdb=" O THR C 440 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE C 448 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU C 449 " --> pdb=" O LEU C 445 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS C 464 " --> pdb=" O ALA C 460 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS C 465 " --> pdb=" O ILE C 461 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS C 466 " --> pdb=" O GLY C 462 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU C 467 " --> pdb=" O SER C 463 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL C 469 " --> pdb=" O LYS C 465 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS C 470 " --> pdb=" O LYS C 466 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU C 472 " --> pdb=" O GLU C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 501 removed outlier: 3.766A pdb=" N ILE C 499 " --> pdb=" O CYS C 495 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER C 500 " --> pdb=" O VAL C 496 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG C 501 " --> pdb=" O ASN C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 510 removed outlier: 3.849A pdb=" N ILE C 510 " --> pdb=" O GLU C 507 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.178A pdb=" N ILE A 362 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LYS A 29 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.178A pdb=" N ILE A 362 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LYS A 29 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE A 25 " --> pdb=" O PHE A 485 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN A 486 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU A 478 " --> pdb=" O ASN A 486 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 36 through 39 Processing sheet with id=AA4, first strand: chain 'A' and resid 50 through 52 Processing sheet with id=AA5, first strand: chain 'A' and resid 54 through 55 removed outlier: 3.555A pdb=" N ILE A 313 " --> pdb=" O GLY A 55 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ILE A 312 " --> pdb=" O ILE A 327 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 61 through 62 removed outlier: 5.636A pdb=" N ILE A 61 " --> pdb=" O ASP A 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 112 through 114 removed outlier: 3.842A pdb=" N THR A 182 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE A 277 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N TYR A 184 " --> pdb=" O THR A 275 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR A 275 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 112 through 114 Processing sheet with id=AA9, first strand: chain 'A' and resid 171 through 176 removed outlier: 4.538A pdb=" N ARG A 211 " --> pdb=" O SER A 265 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 303 through 304 removed outlier: 3.612A pdb=" N GLY A 303 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.195A pdb=" N ILE B 362 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N LYS B 29 " --> pdb=" O ILE B 362 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.195A pdb=" N ILE B 362 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N LYS B 29 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE B 25 " --> pdb=" O PHE B 485 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN B 486 " --> pdb=" O LEU B 478 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU B 478 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 36 through 39 Processing sheet with id=AB5, first strand: chain 'B' and resid 50 through 52 Processing sheet with id=AB6, first strand: chain 'B' and resid 61 through 62 removed outlier: 5.627A pdb=" N ILE B 61 " --> pdb=" O ASP B 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 112 through 114 removed outlier: 3.854A pdb=" N THR B 182 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE B 277 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N TYR B 184 " --> pdb=" O THR B 275 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR B 275 " --> pdb=" O TYR B 184 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 112 through 114 Processing sheet with id=AB9, first strand: chain 'B' and resid 171 through 176 removed outlier: 4.573A pdb=" N ARG B 211 " --> pdb=" O SER B 265 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 303 through 304 removed outlier: 3.610A pdb=" N GLY B 303 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 312 through 313 removed outlier: 6.161A pdb=" N ILE B 312 " --> pdb=" O ILE B 327 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.191A pdb=" N ILE C 362 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N LYS C 29 " --> pdb=" O ILE C 362 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.191A pdb=" N ILE C 362 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N LYS C 29 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE C 25 " --> pdb=" O PHE C 485 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN C 486 " --> pdb=" O LEU C 478 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU C 478 " --> pdb=" O ASN C 486 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 36 through 39 Processing sheet with id=AC6, first strand: chain 'C' and resid 50 through 52 Processing sheet with id=AC7, first strand: chain 'C' and resid 61 through 62 removed outlier: 5.629A pdb=" N ILE C 61 " --> pdb=" O ASP C 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 68 through 70 Processing sheet with id=AC9, first strand: chain 'C' and resid 112 through 114 removed outlier: 3.836A pdb=" N THR C 182 " --> pdb=" O PHE C 277 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE C 277 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N TYR C 184 " --> pdb=" O THR C 275 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N THR C 275 " --> pdb=" O TYR C 184 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 112 through 114 Processing sheet with id=AD2, first strand: chain 'C' and resid 171 through 176 removed outlier: 4.544A pdb=" N ARG C 211 " --> pdb=" O SER C 265 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 303 through 304 removed outlier: 3.627A pdb=" N GLY C 303 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 312 through 313 removed outlier: 6.194A pdb=" N ILE C 312 " --> pdb=" O ILE C 327 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 432 hydrogen bonds defined for protein. 1215 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.68 Time building geometry restraints manager: 1.01 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: 3717 1.34 - 1.46: 2789 1.46 - 1.58: 5158 1.58 - 1.70: 3 1.70 - 1.82: 72 Bond restraints: 11739 Sorted by residual: bond pdb=" C1 BMA D 5 " pdb=" C2 BMA D 5 " ideal model delta sigma weight residual 1.519 1.583 -0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C1 BMA H 5 " pdb=" C2 BMA H 5 " ideal model delta sigma weight residual 1.519 1.583 -0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C1 BMA F 5 " pdb=" C2 BMA F 5 " ideal model delta sigma weight residual 1.519 1.583 -0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C2 BMA D 5 " pdb=" O2 BMA D 5 " ideal model delta sigma weight residual 1.402 1.463 -0.061 2.00e-02 2.50e+03 9.39e+00 bond pdb=" C2 BMA F 5 " pdb=" O2 BMA F 5 " ideal model delta sigma weight residual 1.402 1.463 -0.061 2.00e-02 2.50e+03 9.39e+00 ... (remaining 11734 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 15185 1.35 - 2.70: 532 2.70 - 4.05: 121 4.05 - 5.40: 29 5.40 - 6.75: 24 Bond angle restraints: 15891 Sorted by residual: angle pdb=" N LYS A 379 " pdb=" CA LYS A 379 " pdb=" C LYS A 379 " ideal model delta sigma weight residual 114.75 111.39 3.36 1.26e+00 6.30e-01 7.10e+00 angle pdb=" N LYS B 379 " pdb=" CA LYS B 379 " pdb=" C LYS B 379 " ideal model delta sigma weight residual 114.75 111.40 3.35 1.26e+00 6.30e-01 7.07e+00 angle pdb=" C3 BMA H 3 " pdb=" C2 BMA H 3 " pdb=" O2 BMA H 3 " ideal model delta sigma weight residual 112.95 106.20 6.75 3.00e+00 1.11e-01 5.06e+00 angle pdb=" C3 BMA D 3 " pdb=" C2 BMA D 3 " pdb=" O2 BMA D 3 " ideal model delta sigma weight residual 112.95 106.21 6.74 3.00e+00 1.11e-01 5.05e+00 angle pdb=" C3 BMA F 3 " pdb=" C2 BMA F 3 " pdb=" O2 BMA F 3 " ideal model delta sigma weight residual 112.95 106.23 6.72 3.00e+00 1.11e-01 5.02e+00 ... (remaining 15886 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.45: 6800 22.45 - 44.91: 505 44.91 - 67.36: 27 67.36 - 89.81: 78 89.81 - 112.27: 45 Dihedral angle restraints: 7455 sinusoidal: 3375 harmonic: 4080 Sorted by residual: dihedral pdb=" O4 BMA D 5 " pdb=" C4 BMA D 5 " pdb=" C5 BMA D 5 " pdb=" O5 BMA D 5 " ideal model delta sinusoidal sigma weight residual 288.71 176.44 112.27 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" O4 BMA H 5 " pdb=" C4 BMA H 5 " pdb=" C5 BMA H 5 " pdb=" O5 BMA H 5 " ideal model delta sinusoidal sigma weight residual 288.71 176.73 111.98 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" O4 BMA F 5 " pdb=" C4 BMA F 5 " pdb=" C5 BMA F 5 " pdb=" O5 BMA F 5 " ideal model delta sinusoidal sigma weight residual 288.71 176.73 111.98 1 3.00e+01 1.11e-03 1.47e+01 ... (remaining 7452 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1712 0.088 - 0.176: 154 0.176 - 0.264: 10 0.264 - 0.352: 5 0.352 - 0.439: 3 Chirality restraints: 1884 Sorted by residual: chirality pdb=" C1 NAG C 604 " pdb=" ND2 ASN C 486 " pdb=" C2 NAG C 604 " pdb=" O5 NAG C 604 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.83e+00 chirality pdb=" C1 NAG B 604 " pdb=" ND2 ASN B 486 " pdb=" C2 NAG B 604 " pdb=" O5 NAG B 604 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.80e+00 chirality pdb=" C1 NAG A 604 " pdb=" ND2 ASN A 486 " pdb=" C2 NAG A 604 " pdb=" O5 NAG A 604 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.76e+00 ... (remaining 1881 not shown) Planarity restraints: 2019 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 324 " 0.027 5.00e-02 4.00e+02 4.08e-02 2.67e+00 pdb=" N PRO C 325 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO C 325 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 325 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 324 " 0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO B 325 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 325 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 325 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 324 " 0.026 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO A 325 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 325 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 325 " 0.022 5.00e-02 4.00e+02 ... (remaining 2016 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2390 2.78 - 3.31: 9640 3.31 - 3.84: 16741 3.84 - 4.37: 18983 4.37 - 4.90: 34551 Nonbonded interactions: 82305 Sorted by model distance: nonbonded pdb=" OE2 GLU A 422 " pdb=" ND2 ASN A 426 " model vdw 2.251 3.120 nonbonded pdb=" OE2 GLU C 422 " pdb=" ND2 ASN C 426 " model vdw 2.256 3.120 nonbonded pdb=" OE2 GLU B 422 " pdb=" ND2 ASN B 426 " model vdw 2.258 3.120 nonbonded pdb=" O CYS C 495 " pdb=" OG SER C 498 " model vdw 2.314 3.040 nonbonded pdb=" NZ LYS C 470 " pdb=" OD2 ASP C 479 " model vdw 2.317 3.120 ... (remaining 82300 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } 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: 3.080 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.060 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:6.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5436 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 0.064 11790 Z= 0.199 Angle : 0.678 7.165 16029 Z= 0.315 Chirality : 0.053 0.439 1884 Planarity : 0.003 0.041 2001 Dihedral : 19.133 112.265 4812 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.22), residues: 1425 helix: 2.26 (0.29), residues: 357 sheet: 0.27 (0.35), residues: 231 loop : -2.06 (0.18), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 501 TYR 0.006 0.001 TYR A 509 PHE 0.011 0.001 PHE B 282 TRP 0.012 0.001 TRP B 208 HIS 0.002 0.000 HIS C 489 Details of bonding type rmsd covalent geometry : bond 0.00415 (11739) covalent geometry : angle 0.65069 (15891) SS BOND : bond 0.00161 ( 15) SS BOND : angle 1.24171 ( 30) hydrogen bonds : bond 0.19092 ( 396) hydrogen bonds : angle 5.74247 ( 1215) link_BETA1-2 : bond 0.00589 ( 3) link_BETA1-2 : angle 4.39519 ( 9) link_BETA1-3 : bond 0.00598 ( 3) link_BETA1-3 : angle 3.76030 ( 9) link_BETA1-4 : bond 0.00457 ( 9) link_BETA1-4 : angle 1.69539 ( 27) link_BETA1-6 : bond 0.01452 ( 3) link_BETA1-6 : angle 0.76137 ( 9) link_NAG-ASN : bond 0.00387 ( 18) link_NAG-ASN : angle 2.00083 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.5972 (pttm) cc_final: 0.5680 (pttm) REVERT: A 67 GLN cc_start: 0.6150 (mt0) cc_final: 0.5416 (pt0) REVERT: A 85 GLU cc_start: 0.5991 (tp30) cc_final: 0.5076 (tm-30) REVERT: A 174 GLU cc_start: 0.6289 (mt-10) cc_final: 0.5761 (mt-10) REVERT: A 209 ASP cc_start: 0.5984 (m-30) cc_final: 0.5577 (m-30) REVERT: A 217 GLU cc_start: 0.4596 (tm-30) cc_final: 0.4381 (tm-30) REVERT: A 291 ASP cc_start: 0.6369 (t0) cc_final: 0.5923 (t0) REVERT: A 408 GLN cc_start: 0.4166 (mt0) cc_final: 0.3764 (tp40) REVERT: A 437 GLU cc_start: 0.5118 (mm-30) cc_final: 0.4091 (tm-30) REVERT: B 60 LYS cc_start: 0.6087 (pttt) cc_final: 0.5864 (pttm) REVERT: B 85 GLU cc_start: 0.6413 (tp30) cc_final: 0.5487 (tm-30) REVERT: B 174 GLU cc_start: 0.6143 (mt-10) cc_final: 0.5766 (mt-10) REVERT: B 209 ASP cc_start: 0.5927 (m-30) cc_final: 0.5504 (m-30) REVERT: B 232 GLU cc_start: 0.4959 (tt0) cc_final: 0.4580 (tt0) REVERT: B 260 GLU cc_start: 0.6888 (mp0) cc_final: 0.6531 (mp0) REVERT: B 291 ASP cc_start: 0.6541 (t0) cc_final: 0.6248 (t0) REVERT: B 408 GLN cc_start: 0.4103 (mt0) cc_final: 0.3751 (tp40) REVERT: C 60 LYS cc_start: 0.6412 (pttt) cc_final: 0.6188 (pttm) REVERT: C 67 GLN cc_start: 0.6072 (mt0) cc_final: 0.5467 (pt0) REVERT: C 85 GLU cc_start: 0.6174 (tp30) cc_final: 0.5208 (tm-30) REVERT: C 146 GLU cc_start: 0.6544 (mm-30) cc_final: 0.6290 (mm-30) REVERT: C 174 GLU cc_start: 0.6408 (mt-10) cc_final: 0.6172 (mt-10) REVERT: C 209 ASP cc_start: 0.6213 (m-30) cc_final: 0.5855 (m-30) REVERT: C 232 GLU cc_start: 0.4855 (tt0) cc_final: 0.4109 (mt-10) REVERT: C 291 ASP cc_start: 0.6432 (t0) cc_final: 0.5930 (t0) REVERT: C 408 GLN cc_start: 0.4559 (mt0) cc_final: 0.4157 (tp40) REVERT: C 437 GLU cc_start: 0.5039 (mm-30) cc_final: 0.4009 (tm-30) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.5539 time to fit residues: 100.8728 Evaluate side-chains 133 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.8943 > 50: distance: 9 - 124: 26.295 distance: 16 - 123: 33.815 distance: 60 - 65: 35.175 distance: 65 - 66: 41.144 distance: 66 - 67: 40.524 distance: 66 - 69: 55.943 distance: 67 - 68: 55.972 distance: 67 - 73: 38.728 distance: 69 - 70: 28.570 distance: 70 - 71: 41.386 distance: 70 - 72: 9.056 distance: 73 - 74: 40.929 distance: 74 - 75: 38.739 distance: 74 - 77: 40.304 distance: 75 - 78: 40.806 distance: 78 - 79: 39.707 distance: 79 - 80: 57.207 distance: 79 - 82: 39.525 distance: 80 - 81: 54.682 distance: 80 - 86: 60.361 distance: 83 - 84: 41.175 distance: 83 - 85: 46.308 distance: 86 - 87: 24.345 distance: 87 - 88: 41.790 distance: 87 - 90: 43.590 distance: 88 - 89: 39.937 distance: 88 - 94: 40.347 distance: 91 - 92: 42.477 distance: 94 - 95: 39.010 distance: 95 - 96: 40.456 distance: 96 - 97: 55.947 distance: 96 - 102: 57.017 distance: 98 - 99: 3.050 distance: 99 - 100: 3.195 distance: 99 - 101: 37.412 distance: 102 - 103: 57.130 distance: 103 - 104: 41.107 distance: 104 - 105: 39.322 distance: 107 - 108: 39.179 distance: 107 - 110: 69.560 distance: 108 - 109: 56.853 distance: 108 - 114: 69.270 distance: 111 - 112: 55.531 distance: 111 - 113: 40.115 distance: 114 - 115: 39.871 distance: 115 - 116: 38.916 distance: 116 - 117: 39.430 distance: 116 - 118: 40.151 distance: 119 - 120: 57.983 distance: 119 - 122: 40.210 distance: 120 - 121: 56.238 distance: 120 - 124: 60.776 distance: 122 - 123: 56.184 distance: 124 - 125: 60.476 distance: 125 - 126: 15.587 distance: 126 - 127: 26.005 distance: 126 - 135: 27.741 distance: 128 - 129: 42.326 distance: 129 - 130: 24.488 distance: 129 - 131: 17.829 distance: 130 - 132: 70.431 distance: 131 - 133: 57.887 distance: 132 - 134: 53.015 distance: 133 - 134: 52.732