Starting phenix.real_space_refine on Mon Aug 25 22:14:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j77_61196/08_2025/9j77_61196.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j77_61196/08_2025/9j77_61196.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j77_61196/08_2025/9j77_61196.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j77_61196/08_2025/9j77_61196.map" model { file = "/net/cci-nas-00/data/ceres_data/9j77_61196/08_2025/9j77_61196.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j77_61196/08_2025/9j77_61196.cif" } resolution = 3.56 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= 0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6261 atoms to isotropic. 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 Zn 6 6.06 5 S 182 5.16 5 C 16576 2.51 5 N 4544 2.21 5 O 4901 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s 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: 26209 Number of models: 1 Model: "" Number of chains: 14 Chain: "G" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "H" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 759 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 8, 'TRANS': 87} Chain breaks: 1 Chain: "I" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 598 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 5947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 725, 5947 Classifications: {'peptide': 725} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 705} Chain breaks: 1 Chain: "C" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "D" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 759 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 8, 'TRANS': 87} Chain breaks: 1 Chain: "J" Number of atoms: 4932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4932 Classifications: {'peptide': 627} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 611} Chain: "E" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 703 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 4932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4932 Classifications: {'peptide': 627} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 611} Chain: "A" Number of atoms: 5953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5953 Classifications: {'peptide': 726} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 706} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 50 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'UNK:plan-1': 10} Unresolved non-hydrogen planarities: 10 Chain: "L" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 50 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'UNK:plan-1': 10} Unresolved non-hydrogen planarities: 10 Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1762 SG CYS I 53 46.427 71.722 86.097 1.00 90.27 S ATOM 1785 SG CYS I 56 49.875 72.606 87.957 1.00 99.16 S ATOM 1813 SG CYS I 68 48.301 69.099 88.163 1.00 86.92 S ATOM 1676 SG CYS I 42 42.345 67.690 81.363 1.00 80.52 S ATOM 1695 SG CYS I 45 42.937 71.493 81.054 1.00 89.98 S ATOM 1931 SG CYS I 83 41.945 70.007 84.421 1.00 91.34 S ATOM 1863 SG CYS I 75 36.823 55.808 81.419 1.00117.13 S ATOM 2027 SG CYS I 94 35.211 57.851 83.556 1.00118.96 S ATOM 14789 SG CYS E 53 17.339 119.410 57.731 1.00 85.23 S ATOM 14812 SG CYS E 56 13.849 119.625 59.303 1.00 99.64 S ATOM 14896 SG CYS E 68 16.916 119.269 61.548 1.00 89.56 S ATOM 14703 SG CYS E 42 25.247 118.863 57.695 1.00 60.90 S ATOM 14722 SG CYS E 45 22.322 121.187 56.734 1.00 66.02 S ATOM 15014 SG CYS E 83 21.765 117.678 56.358 1.00 64.24 S ATOM 14946 SG CYS E 75 32.780 108.087 60.467 1.00 46.34 S ATOM 15110 SG CYS E 94 31.255 109.815 57.094 1.00 34.12 S Time building chain proxies: 5.50, per 1000 atoms: 0.21 Number of scatterers: 26209 At special positions: 0 Unit cell: (138.58, 177.12, 205, 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) Zn 6 29.99 S 182 16.00 O 4901 8.00 N 4544 7.00 C 16576 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: 2.19 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 200 " pdb="ZN ZN E 200 " - pdb=" NE2 HIS E 82 " pdb="ZN ZN E 200 " - pdb=" SG CYS E 56 " pdb="ZN ZN E 200 " - pdb=" SG CYS E 53 " pdb="ZN ZN E 200 " - pdb=" SG CYS E 68 " pdb=" ZN E 201 " pdb="ZN ZN E 201 " - pdb=" ND1 HIS E 80 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 45 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 83 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 42 " pdb=" ZN E 202 " pdb="ZN ZN E 202 " - pdb=" SG CYS E 94 " pdb="ZN ZN E 202 " - pdb=" SG CYS E 75 " pdb="ZN ZN E 202 " - pdb=" ND1 HIS E 77 " pdb=" ZN I 200 " pdb="ZN ZN I 200 " - pdb=" ND1 HIS I 82 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 68 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 53 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 56 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" ND1 HIS I 80 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 83 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 45 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 94 " pdb="ZN ZN I 202 " - pdb=" ND1 HIS I 77 " Number of angles added : 12 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6288 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 14 sheets defined 62.0% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'G' and resid 33 through 37 Processing helix chain 'G' and resid 39 through 47 removed outlier: 3.503A pdb=" N LYS G 43 " --> pdb=" O SER G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 83 Processing helix chain 'G' and resid 102 through 111 Processing helix chain 'H' and resid 23 through 36 removed outlier: 4.174A pdb=" N LEU H 27 " --> pdb=" O THR H 23 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE H 34 " --> pdb=" O ILE H 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 58 removed outlier: 4.226A pdb=" N ALA I 58 " --> pdb=" O ILE I 54 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 91 Processing helix chain 'B' and resid 9 through 26 removed outlier: 3.821A pdb=" N THR B 13 " --> pdb=" O ASP B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 47 Processing helix chain 'B' and resid 54 through 79 Processing helix chain 'B' and resid 82 through 105 Processing helix chain 'B' and resid 105 through 112 Processing helix chain 'B' and resid 138 through 152 removed outlier: 3.627A pdb=" N VAL B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 172 Processing helix chain 'B' and resid 177 through 187 Processing helix chain 'B' and resid 200 through 207 Processing helix chain 'B' and resid 207 through 230 Processing helix chain 'B' and resid 231 through 254 Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 258 through 271 removed outlier: 3.578A pdb=" N VAL B 262 " --> pdb=" O SER B 258 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE B 263 " --> pdb=" O TYR B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 289 removed outlier: 3.603A pdb=" N LEU B 278 " --> pdb=" O HIS B 274 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N HIS B 283 " --> pdb=" O HIS B 279 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ASN B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 304 removed outlier: 3.580A pdb=" N LEU B 300 " --> pdb=" O ASN B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 328 removed outlier: 4.045A pdb=" N MET B 311 " --> pdb=" O GLY B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 358 Processing helix chain 'B' and resid 361 through 377 Processing helix chain 'B' and resid 386 through 400 Processing helix chain 'B' and resid 407 through 424 removed outlier: 4.119A pdb=" N THR B 420 " --> pdb=" O THR B 416 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL B 421 " --> pdb=" O SER B 417 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR B 424 " --> pdb=" O THR B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 445 removed outlier: 3.757A pdb=" N PHE B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 466 Processing helix chain 'B' and resid 470 through 482 Processing helix chain 'B' and resid 482 through 496 Processing helix chain 'B' and resid 530 through 548 removed outlier: 3.518A pdb=" N GLU B 534 " --> pdb=" O PRO B 530 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LYS B 535 " --> pdb=" O GLN B 531 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N SER B 536 " --> pdb=" O GLU B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 559 No H-bonds generated for 'chain 'B' and resid 557 through 559' Processing helix chain 'B' and resid 579 through 591 removed outlier: 3.511A pdb=" N SER B 591 " --> pdb=" O ALA B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 603 Processing helix chain 'B' and resid 606 through 620 Processing helix chain 'B' and resid 661 through 692 Processing helix chain 'B' and resid 695 through 708 Processing helix chain 'B' and resid 714 through 728 Processing helix chain 'C' and resid 33 through 37 Processing helix chain 'C' and resid 39 through 47 Processing helix chain 'C' and resid 66 through 83 Processing helix chain 'C' and resid 102 through 111 Processing helix chain 'D' and resid 24 through 36 Processing helix chain 'J' and resid 2 through 15 Processing helix chain 'J' and resid 17 through 24 Processing helix chain 'J' and resid 29 through 37 Processing helix chain 'J' and resid 48 through 56 Processing helix chain 'J' and resid 58 through 69 removed outlier: 4.146A pdb=" N VAL J 62 " --> pdb=" O HIS J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 98 removed outlier: 3.643A pdb=" N CYS J 94 " --> pdb=" O THR J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 110 removed outlier: 3.700A pdb=" N VAL J 104 " --> pdb=" O HIS J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 132 removed outlier: 3.911A pdb=" N ALA J 127 " --> pdb=" O THR J 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 143 Processing helix chain 'J' and resid 156 through 163 Processing helix chain 'J' and resid 166 through 175 Processing helix chain 'J' and resid 191 through 196 removed outlier: 3.733A pdb=" N GLU J 196 " --> pdb=" O HIS J 192 " (cutoff:3.500A) Processing helix chain 'J' and resid 199 through 209 Processing helix chain 'J' and resid 221 through 229 Processing helix chain 'J' and resid 231 through 240 Processing helix chain 'J' and resid 244 through 262 removed outlier: 4.094A pdb=" N SER J 248 " --> pdb=" O CYS J 244 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA J 261 " --> pdb=" O GLY J 257 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN J 262 " --> pdb=" O ALA J 258 " (cutoff:3.500A) Processing helix chain 'J' and resid 268 through 284 Processing helix chain 'J' and resid 299 through 303 Processing helix chain 'J' and resid 310 through 317 removed outlier: 3.549A pdb=" N LEU J 314 " --> pdb=" O ASN J 310 " (cutoff:3.500A) Processing helix chain 'J' and resid 320 through 337 Processing helix chain 'J' and resid 344 through 357 Processing helix chain 'J' and resid 359 through 377 Processing helix chain 'J' and resid 381 through 398 Processing helix chain 'J' and resid 403 through 428 Processing helix chain 'J' and resid 432 through 456 Processing helix chain 'J' and resid 460 through 476 Processing helix chain 'J' and resid 486 through 493 removed outlier: 3.533A pdb=" N ALA J 491 " --> pdb=" O LEU J 487 " (cutoff:3.500A) Processing helix chain 'J' and resid 501 through 506 Processing helix chain 'J' and resid 511 through 521 Processing helix chain 'J' and resid 534 through 541 removed outlier: 3.678A pdb=" N ILE J 538 " --> pdb=" O SER J 534 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE J 539 " --> pdb=" O ALA J 535 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN J 541 " --> pdb=" O HIS J 537 " (cutoff:3.500A) Processing helix chain 'J' and resid 548 through 563 removed outlier: 3.808A pdb=" N SER J 558 " --> pdb=" O SER J 554 " (cutoff:3.500A) Processing helix chain 'J' and resid 577 through 581 removed outlier: 4.243A pdb=" N THR J 581 " --> pdb=" O ASP J 578 " (cutoff:3.500A) Processing helix chain 'J' and resid 582 through 593 Processing helix chain 'J' and resid 596 through 609 Processing helix chain 'J' and resid 617 through 627 removed outlier: 4.110A pdb=" N GLU J 622 " --> pdb=" O ARG J 618 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N PHE J 623 " --> pdb=" O THR J 619 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 58 removed outlier: 4.056A pdb=" N ALA E 58 " --> pdb=" O ILE E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 89 Processing helix chain 'F' and resid 2 through 14 removed outlier: 3.532A pdb=" N VAL F 8 " --> pdb=" O LEU F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 23 removed outlier: 3.677A pdb=" N LEU F 20 " --> pdb=" O LYS F 16 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA F 22 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU F 23 " --> pdb=" O THR F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 37 removed outlier: 3.945A pdb=" N ILE F 32 " --> pdb=" O SER F 28 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG F 33 " --> pdb=" O GLU F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 56 removed outlier: 3.612A pdb=" N ILE F 52 " --> pdb=" O THR F 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA F 53 " --> pdb=" O PRO F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 69 removed outlier: 3.736A pdb=" N VAL F 62 " --> pdb=" O HIS F 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU F 64 " --> pdb=" O LYS F 60 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU F 65 " --> pdb=" O VAL F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 98 removed outlier: 3.958A pdb=" N CYS F 94 " --> pdb=" O THR F 90 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA F 96 " --> pdb=" O LEU F 92 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY F 97 " --> pdb=" O TRP F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 110 removed outlier: 3.729A pdb=" N VAL F 104 " --> pdb=" O HIS F 100 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS F 105 " --> pdb=" O PHE F 101 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU F 106 " --> pdb=" O GLU F 102 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU F 107 " --> pdb=" O VAL F 103 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N HIS F 110 " --> pdb=" O LEU F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 132 removed outlier: 4.056A pdb=" N ALA F 127 " --> pdb=" O THR F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 143 removed outlier: 3.533A pdb=" N GLU F 142 " --> pdb=" O LYS F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 164 removed outlier: 3.569A pdb=" N ILE F 160 " --> pdb=" O THR F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 174 removed outlier: 3.834A pdb=" N VAL F 170 " --> pdb=" O HIS F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 177 No H-bonds generated for 'chain 'F' and resid 175 through 177' Processing helix chain 'F' and resid 199 through 210 removed outlier: 3.593A pdb=" N VAL F 203 " --> pdb=" O HIS F 199 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS F 204 " --> pdb=" O ILE F 200 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS F 208 " --> pdb=" O LYS F 204 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TRP F 209 " --> pdb=" O GLU F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 229 Processing helix chain 'F' and resid 231 through 239 removed outlier: 3.663A pdb=" N GLU F 236 " --> pdb=" O ALA F 232 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU F 237 " --> pdb=" O ASP F 233 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU F 239 " --> pdb=" O VAL F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 262 removed outlier: 3.716A pdb=" N ILE F 250 " --> pdb=" O ARG F 246 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU F 251 " --> pdb=" O ARG F 247 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA F 252 " --> pdb=" O SER F 248 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU F 253 " --> pdb=" O ARG F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 284 Processing helix chain 'F' and resid 310 through 317 removed outlier: 3.823A pdb=" N LEU F 314 " --> pdb=" O ASN F 310 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE F 317 " --> pdb=" O GLU F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 337 removed outlier: 3.726A pdb=" N ILE F 330 " --> pdb=" O MET F 326 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL F 331 " --> pdb=" O GLU F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 344 through 356 Processing helix chain 'F' and resid 360 through 377 Processing helix chain 'F' and resid 381 through 398 Processing helix chain 'F' and resid 403 through 428 Processing helix chain 'F' and resid 432 through 456 Processing helix chain 'F' and resid 460 through 478 Processing helix chain 'F' and resid 486 through 493 Processing helix chain 'F' and resid 502 through 507 Processing helix chain 'F' and resid 511 through 522 Processing helix chain 'F' and resid 535 through 540 removed outlier: 3.524A pdb=" N ILE F 539 " --> pdb=" O ALA F 535 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 563 Processing helix chain 'F' and resid 584 through 591 Processing helix chain 'F' and resid 596 through 609 Processing helix chain 'F' and resid 617 through 625 Processing helix chain 'A' and resid 9 through 26 Processing helix chain 'A' and resid 31 through 48 Processing helix chain 'A' and resid 53 through 79 removed outlier: 3.657A pdb=" N SER A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 105 Processing helix chain 'A' and resid 105 through 112 Processing helix chain 'A' and resid 138 through 151 removed outlier: 3.757A pdb=" N LEU A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 164 removed outlier: 3.532A pdb=" N ILE A 160 " --> pdb=" O GLN A 156 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ARG A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET A 162 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 164 " --> pdb=" O ILE A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 172 removed outlier: 3.784A pdb=" N ASP A 170 " --> pdb=" O GLU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 191 removed outlier: 3.963A pdb=" N VAL A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 195 Processing helix chain 'A' and resid 200 through 207 removed outlier: 3.557A pdb=" N PHE A 207 " --> pdb=" O TYR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 227 removed outlier: 3.697A pdb=" N GLN A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 254 removed outlier: 3.684A pdb=" N MET A 236 " --> pdb=" O CYS A 232 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 258 through 271 removed outlier: 3.547A pdb=" N ILE A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 281 Processing helix chain 'A' and resid 281 through 288 Processing helix chain 'A' and resid 290 through 304 removed outlier: 3.507A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA A 303 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 327 removed outlier: 4.130A pdb=" N MET A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN A 313 " --> pdb=" O PRO A 309 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 324 " --> pdb=" O HIS A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 353 removed outlier: 3.775A pdb=" N VAL A 340 " --> pdb=" O PRO A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 377 removed outlier: 3.912A pdb=" N ALA A 367 " --> pdb=" O HIS A 363 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN A 377 " --> pdb=" O THR A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 400 Processing helix chain 'A' and resid 407 through 417 removed outlier: 3.894A pdb=" N SER A 417 " --> pdb=" O ASP A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 423 removed outlier: 4.021A pdb=" N VAL A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 444 Processing helix chain 'A' and resid 450 through 466 removed outlier: 3.713A pdb=" N GLU A 454 " --> pdb=" O SER A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 496 removed outlier: 3.546A pdb=" N HIS A 474 " --> pdb=" O THR A 470 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ALA A 484 " --> pdb=" O MET A 480 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ASP A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS A 495 " --> pdb=" O ASN A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 548 Processing helix chain 'A' and resid 579 through 591 removed outlier: 3.745A pdb=" N VAL A 584 " --> pdb=" O TYR A 580 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER A 591 " --> pdb=" O ALA A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 603 removed outlier: 3.626A pdb=" N SER A 602 " --> pdb=" O GLU A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 620 removed outlier: 4.081A pdb=" N LYS A 612 " --> pdb=" O LYS A 608 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU A 617 " --> pdb=" O THR A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 690 removed outlier: 4.161A pdb=" N GLN A 667 " --> pdb=" O GLN A 663 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 672 " --> pdb=" O THR A 668 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASP A 673 " --> pdb=" O ARG A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 706 Processing helix chain 'A' and resid 714 through 728 Processing helix chain 'K' and resid 2 through 9 removed outlier: 4.110A pdb=" N UNK K 9 " --> pdb=" O UNK K 5 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 137 Processing sheet with id=AA1, first strand: chain 'G' and resid 28 through 32 removed outlier: 3.756A pdb=" N VAL G 60 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 13 through 18 removed outlier: 3.519A pdb=" N GLY H 76 " --> pdb=" O TYR H 45 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 506 through 507 removed outlier: 4.167A pdb=" N LYS I 26 " --> pdb=" O GLU A 563 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 510 through 513 removed outlier: 5.651A pdb=" N ALA I 31 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR A 554 " --> pdb=" O LEU I 32 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 41 through 42 removed outlier: 3.507A pdb=" N ASN I 47 " --> pdb=" O CYS I 42 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 70 through 71 Processing sheet with id=AA7, first strand: chain 'B' and resid 510 through 513 removed outlier: 3.708A pdb=" N ALA E 31 " --> pdb=" O TYR B 510 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 574 through 578 removed outlier: 6.402A pdb=" N THR B 561 " --> pdb=" O TRP E 27 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N TRP E 27 " --> pdb=" O THR B 561 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU E 23 " --> pdb=" O LYS B 565 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 60 through 61 removed outlier: 5.008A pdb=" N LYS C 32 " --> pdb=" O PHE D 15 " (cutoff:3.500A) removed outlier: 10.548A pdb=" N ASP D 17 " --> pdb=" O LYS C 32 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA D 73 " --> pdb=" O PHE D 4 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA D 78 " --> pdb=" O ARG D 43 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG D 43 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 40 through 42 Processing sheet with id=AB2, first strand: chain 'E' and resid 70 through 72 Processing sheet with id=AB3, first strand: chain 'F' and resid 40 through 42 Processing sheet with id=AB4, first strand: chain 'A' and resid 623 through 625 Processing sheet with id=AB5, first strand: chain 'A' and resid 693 through 694 1382 hydrogen bonds defined for protein. 4086 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: 4.13 Time building geometry restraints manager: 2.88 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: 8550 1.34 - 1.46: 3738 1.46 - 1.58: 14135 1.58 - 1.70: 0 1.70 - 1.81: 284 Bond restraints: 26707 Sorted by residual: bond pdb=" C LEU A 308 " pdb=" N PRO A 309 " ideal model delta sigma weight residual 1.334 1.370 -0.036 2.34e-02 1.83e+03 2.33e+00 bond pdb=" CA ASN C 85 " pdb=" CB ASN C 85 " ideal model delta sigma weight residual 1.525 1.545 -0.020 1.77e-02 3.19e+03 1.26e+00 bond pdb=" C ALA B 387 " pdb=" N PRO B 388 " ideal model delta sigma weight residual 1.335 1.350 -0.015 1.36e-02 5.41e+03 1.21e+00 bond pdb=" C LEU B 308 " pdb=" N PRO B 309 " ideal model delta sigma weight residual 1.335 1.349 -0.014 1.28e-02 6.10e+03 1.19e+00 bond pdb=" CB PHE B 39 " pdb=" CG PHE B 39 " ideal model delta sigma weight residual 1.502 1.477 0.025 2.30e-02 1.89e+03 1.17e+00 ... (remaining 26702 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 35596 1.98 - 3.97: 408 3.97 - 5.95: 73 5.95 - 7.94: 16 7.94 - 9.92: 3 Bond angle restraints: 36096 Sorted by residual: angle pdb=" N VAL B 620 " pdb=" CA VAL B 620 " pdb=" C VAL B 620 " ideal model delta sigma weight residual 112.29 107.29 5.00 9.40e-01 1.13e+00 2.83e+01 angle pdb=" N GLN J 420 " pdb=" CA GLN J 420 " pdb=" CB GLN J 420 " ideal model delta sigma weight residual 110.28 115.92 -5.64 1.55e+00 4.16e-01 1.32e+01 angle pdb=" C TYR J 84 " pdb=" N VAL J 85 " pdb=" CA VAL J 85 " ideal model delta sigma weight residual 121.97 128.49 -6.52 1.80e+00 3.09e-01 1.31e+01 angle pdb=" C TYR F 84 " pdb=" N VAL F 85 " pdb=" CA VAL F 85 " ideal model delta sigma weight residual 121.97 128.49 -6.52 1.80e+00 3.09e-01 1.31e+01 angle pdb=" CA TRP B 35 " pdb=" CB TRP B 35 " pdb=" CG TRP B 35 " ideal model delta sigma weight residual 113.60 120.38 -6.78 1.90e+00 2.77e-01 1.27e+01 ... (remaining 36091 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 14382 17.80 - 35.60: 1527 35.60 - 53.41: 257 53.41 - 71.21: 58 71.21 - 89.01: 29 Dihedral angle restraints: 16253 sinusoidal: 6588 harmonic: 9665 Sorted by residual: dihedral pdb=" CA VAL A 47 " pdb=" C VAL A 47 " pdb=" N ALA A 48 " pdb=" CA ALA A 48 " ideal model delta harmonic sigma weight residual -180.00 -158.42 -21.58 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA ALA B 522 " pdb=" C ALA B 522 " pdb=" N PRO B 523 " pdb=" CA PRO B 523 " ideal model delta harmonic sigma weight residual 180.00 162.17 17.83 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA PHE B 188 " pdb=" C PHE B 188 " pdb=" N VAL B 189 " pdb=" CA VAL B 189 " ideal model delta harmonic sigma weight residual 180.00 162.36 17.64 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 16250 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 3078 0.044 - 0.089: 790 0.089 - 0.133: 179 0.133 - 0.177: 14 0.177 - 0.222: 3 Chirality restraints: 4064 Sorted by residual: chirality pdb=" CB ILE A 653 " pdb=" CA ILE A 653 " pdb=" CG1 ILE A 653 " pdb=" CG2 ILE A 653 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CB VAL A 620 " pdb=" CA VAL A 620 " pdb=" CG1 VAL A 620 " pdb=" CG2 VAL A 620 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB VAL B 620 " pdb=" CA VAL B 620 " pdb=" CG1 VAL B 620 " pdb=" CG2 VAL B 620 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.64e-01 ... (remaining 4061 not shown) Planarity restraints: 4635 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 522 " 0.045 5.00e-02 4.00e+02 6.74e-02 7.26e+00 pdb=" N PRO B 523 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 523 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 523 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 183 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.89e+00 pdb=" C GLY B 183 " -0.038 2.00e-02 2.50e+03 pdb=" O GLY B 183 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL B 184 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR J 48 " -0.036 5.00e-02 4.00e+02 5.40e-02 4.66e+00 pdb=" N PRO J 49 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO J 49 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO J 49 " -0.030 5.00e-02 4.00e+02 ... (remaining 4632 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 256 2.62 - 3.19: 22806 3.19 - 3.76: 42671 3.76 - 4.33: 55873 4.33 - 4.90: 91631 Nonbonded interactions: 213237 Sorted by model distance: nonbonded pdb=" OD1 ASP E 97 " pdb="ZN ZN E 202 " model vdw 2.055 2.230 nonbonded pdb=" O CYS J 244 " pdb=" OG SER J 248 " model vdw 2.198 3.040 nonbonded pdb=" OH TYR J 275 " pdb=" O ILE F 546 " model vdw 2.219 3.040 nonbonded pdb=" OH TYR C 79 " pdb=" O PRO C 91 " model vdw 2.238 3.040 nonbonded pdb=" NE1 TRP E 87 " pdb=" O VAL E 93 " model vdw 2.280 3.120 ... (remaining 213232 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 1 through 115 or resid 135 through 744)) selection = (chain 'B' and (resid 1 through 75 or (resid 76 and (name N or name CA or name C \ or name O or name CB )) or resid 77 through 744)) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'E' and (resid 24 through 59 or resid 68 through 101 or (resid 102 and (n \ ame N or name CA or name C or name O or name CB )) or resid 103 through 104 or r \ esid 200 through 202)) selection = chain 'I' } ncs_group { reference = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 19.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.730 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: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 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 : 0.003 0.036 26729 Z= 0.125 Angle : 0.568 10.635 36108 Z= 0.302 Chirality : 0.041 0.222 4064 Planarity : 0.004 0.067 4635 Dihedral : 15.139 89.009 9965 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -1.33 (0.14), residues: 3218 helix: -0.29 (0.11), residues: 1898 sheet: -1.33 (0.56), residues: 79 loop : -1.66 (0.17), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 99 TYR 0.017 0.001 TYR F 472 PHE 0.021 0.001 PHE B 507 TRP 0.016 0.001 TRP I 33 HIS 0.006 0.001 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00255 (26707) covalent geometry : angle 0.56377 (36096) hydrogen bonds : bond 0.18949 ( 1382) hydrogen bonds : angle 6.47056 ( 4086) metal coordination : bond 0.00742 ( 22) metal coordination : angle 3.79513 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 622 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 20 LYS cc_start: 0.8591 (tttp) cc_final: 0.7862 (tmtt) REVERT: G 61 ASN cc_start: 0.7887 (t0) cc_final: 0.7633 (t0) REVERT: I 84 ILE cc_start: 0.7873 (mm) cc_final: 0.7645 (tp) REVERT: B 7 VAL cc_start: 0.8687 (t) cc_final: 0.8376 (m) REVERT: B 362 GLN cc_start: 0.8511 (tp40) cc_final: 0.7864 (tm-30) REVERT: B 377 ASN cc_start: 0.5930 (t0) cc_final: 0.5496 (t0) REVERT: B 379 ARG cc_start: 0.7678 (tpp80) cc_final: 0.7460 (ttt90) REVERT: B 389 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7535 (tm-30) REVERT: B 652 LYS cc_start: 0.8939 (mttm) cc_final: 0.8719 (ttpt) REVERT: B 678 MET cc_start: 0.8010 (tpt) cc_final: 0.7781 (tpt) REVERT: B 741 TYR cc_start: 0.5042 (m-80) cc_final: 0.4298 (m-80) REVERT: D 2 ASP cc_start: 0.6016 (p0) cc_final: 0.5757 (m-30) REVERT: D 23 THR cc_start: 0.8327 (t) cc_final: 0.8111 (p) REVERT: J 93 TRP cc_start: 0.6609 (t60) cc_final: 0.6307 (t60) REVERT: J 196 GLU cc_start: 0.7321 (tp30) cc_final: 0.6990 (tp30) REVERT: E 62 SER cc_start: 0.4758 (p) cc_final: 0.4340 (t) REVERT: E 105 LYS cc_start: 0.6304 (mmpt) cc_final: 0.5006 (mtmm) REVERT: F 358 MET cc_start: 0.7902 (mmt) cc_final: 0.6745 (tmm) REVERT: F 391 VAL cc_start: 0.9284 (p) cc_final: 0.9046 (p) REVERT: F 468 ASN cc_start: 0.8279 (m-40) cc_final: 0.7388 (m-40) REVERT: A 236 MET cc_start: 0.8925 (mtm) cc_final: 0.8349 (mtm) REVERT: A 297 MET cc_start: 0.8591 (tpp) cc_final: 0.7622 (tpp) REVERT: A 396 ASP cc_start: 0.7836 (t70) cc_final: 0.7449 (t0) REVERT: A 604 GLN cc_start: 0.7894 (mm-40) cc_final: 0.7370 (tp40) outliers start: 0 outliers final: 0 residues processed: 622 average time/residue: 0.1692 time to fit residues: 162.9611 Evaluate side-chains 378 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 378 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.0010 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.0470 overall best weight: 0.4486 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN ** I 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 GLN ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 155 ASN J 476 HIS J 553 HIS A 204 GLN A 274 HIS A 292 ASN A 377 ASN A 487 ASN A 497 GLN A 547 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.135976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.106221 restraints weight = 56916.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.104589 restraints weight = 84527.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.106338 restraints weight = 70423.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.106602 restraints weight = 42455.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.108188 restraints weight = 36891.202| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26729 Z= 0.136 Angle : 0.594 13.736 36108 Z= 0.307 Chirality : 0.040 0.249 4064 Planarity : 0.004 0.055 4635 Dihedral : 3.976 20.325 3546 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.60 % Allowed : 9.41 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -0.39 (0.15), residues: 3218 helix: 0.56 (0.12), residues: 1950 sheet: -1.22 (0.52), residues: 87 loop : -1.54 (0.17), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 37 TYR 0.025 0.001 TYR J 472 PHE 0.025 0.002 PHE J 626 TRP 0.021 0.001 TRP J 209 HIS 0.019 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00295 (26707) covalent geometry : angle 0.58682 (36096) hydrogen bonds : bond 0.04441 ( 1382) hydrogen bonds : angle 4.55000 ( 4086) metal coordination : bond 0.01674 ( 22) metal coordination : angle 5.09578 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 415 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 20 LYS cc_start: 0.8292 (tttp) cc_final: 0.7081 (tttm) REVERT: I 55 GLU cc_start: 0.6920 (mm-30) cc_final: 0.6595 (mt-10) REVERT: B 7 VAL cc_start: 0.8365 (t) cc_final: 0.8032 (m) REVERT: B 362 GLN cc_start: 0.8036 (tp40) cc_final: 0.7754 (tm-30) REVERT: B 377 ASN cc_start: 0.5992 (t0) cc_final: 0.5503 (t0) REVERT: B 741 TYR cc_start: 0.5165 (m-80) cc_final: 0.4553 (m-80) REVERT: C 69 VAL cc_start: 0.8663 (m) cc_final: 0.8285 (t) REVERT: J 196 GLU cc_start: 0.7051 (tp30) cc_final: 0.6748 (tp30) REVERT: J 277 TYR cc_start: 0.8136 (t80) cc_final: 0.7907 (t80) REVERT: J 499 ASP cc_start: 0.6119 (OUTLIER) cc_final: 0.5892 (t0) REVERT: J 593 MET cc_start: 0.7211 (mtm) cc_final: 0.6925 (mtp) REVERT: E 62 SER cc_start: 0.4699 (p) cc_final: 0.4218 (t) REVERT: E 105 LYS cc_start: 0.6434 (mmpt) cc_final: 0.5244 (mtmm) REVERT: F 280 MET cc_start: 0.2090 (tpp) cc_final: 0.1832 (ttm) REVERT: A 236 MET cc_start: 0.8914 (mtm) cc_final: 0.8387 (mtt) REVERT: A 297 MET cc_start: 0.8513 (tpp) cc_final: 0.7539 (tpp) REVERT: A 396 ASP cc_start: 0.7991 (t70) cc_final: 0.7538 (t0) REVERT: A 604 GLN cc_start: 0.8014 (mm-40) cc_final: 0.7757 (tp40) outliers start: 46 outliers final: 28 residues processed: 438 average time/residue: 0.1784 time to fit residues: 123.3721 Evaluate side-chains 369 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 340 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain J residue 153 TYR Chi-restraints excluded: chain J residue 237 LEU Chi-restraints excluded: chain J residue 268 ASP Chi-restraints excluded: chain J residue 499 ASP Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 465 CYS Chi-restraints excluded: chain A residue 495 LYS Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 547 HIS Chi-restraints excluded: chain A residue 661 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 180 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 chunk 174 optimal weight: 0.7980 chunk 276 optimal weight: 0.6980 chunk 249 optimal weight: 1.9990 chunk 302 optimal weight: 8.9990 chunk 153 optimal weight: 0.9990 chunk 277 optimal weight: 0.5980 chunk 265 optimal weight: 0.9980 chunk 33 optimal weight: 0.2980 chunk 5 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN B 36 ASN ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 HIS B 706 GLN C 27 HIS ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 375 GLN A 359 ASN A 445 HIS A 547 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.134869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.101770 restraints weight = 57363.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.097861 restraints weight = 54428.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.098920 restraints weight = 50742.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.099660 restraints weight = 37159.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.099885 restraints weight = 33113.465| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26729 Z= 0.149 Angle : 0.570 12.564 36108 Z= 0.293 Chirality : 0.040 0.251 4064 Planarity : 0.004 0.057 4635 Dihedral : 3.958 19.062 3546 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.95 % Allowed : 11.60 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % 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: -0.06 (0.15), residues: 3218 helix: 0.88 (0.12), residues: 1945 sheet: -1.10 (0.54), residues: 79 loop : -1.48 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 32 TYR 0.021 0.001 TYR G 79 PHE 0.023 0.002 PHE J 626 TRP 0.034 0.002 TRP J 209 HIS 0.011 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00337 (26707) covalent geometry : angle 0.56304 (36096) hydrogen bonds : bond 0.04070 ( 1382) hydrogen bonds : angle 4.35971 ( 4086) metal coordination : bond 0.01698 ( 22) metal coordination : angle 4.75364 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 366 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 49 GLN cc_start: 0.6710 (OUTLIER) cc_final: 0.6088 (pm20) REVERT: I 55 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6761 (mt-10) REVERT: B 7 VAL cc_start: 0.8380 (t) cc_final: 0.8049 (m) REVERT: B 362 GLN cc_start: 0.8082 (tp40) cc_final: 0.7766 (tm-30) REVERT: B 741 TYR cc_start: 0.5356 (m-80) cc_final: 0.4576 (m-80) REVERT: J 117 THR cc_start: 0.6678 (p) cc_final: 0.6413 (p) REVERT: J 196 GLU cc_start: 0.7222 (tp30) cc_final: 0.6899 (tp30) REVERT: E 50 MET cc_start: 0.7380 (mmm) cc_final: 0.7134 (mmt) REVERT: E 62 SER cc_start: 0.4559 (p) cc_final: 0.4146 (t) REVERT: E 105 LYS cc_start: 0.6431 (mmpt) cc_final: 0.5274 (mtmm) REVERT: A 236 MET cc_start: 0.8871 (mtm) cc_final: 0.8619 (mtm) REVERT: A 297 MET cc_start: 0.8454 (tpp) cc_final: 0.7668 (tpp) REVERT: A 396 ASP cc_start: 0.7887 (t70) cc_final: 0.7455 (t0) REVERT: A 539 MET cc_start: 0.7837 (tpp) cc_final: 0.7566 (tpt) REVERT: A 604 GLN cc_start: 0.8198 (mm-40) cc_final: 0.7675 (tp40) REVERT: A 694 LEU cc_start: 0.8120 (mt) cc_final: 0.7844 (mt) outliers start: 56 outliers final: 34 residues processed: 390 average time/residue: 0.1780 time to fit residues: 111.3376 Evaluate side-chains 360 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 325 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 49 GLN Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 56 CYS Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain J residue 153 TYR Chi-restraints excluded: chain J residue 220 MET Chi-restraints excluded: chain J residue 237 LEU Chi-restraints excluded: chain J residue 268 ASP Chi-restraints excluded: chain J residue 501 PHE Chi-restraints excluded: chain J residue 575 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain F residue 519 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 495 LYS Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 547 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- 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: 51.2917 > 50: distance: 65 - 85: 3.450 distance: 86 - 87: 5.570 distance: 87 - 88: 3.118 distance: 87 - 93: 5.150 distance: 88 - 118: 7.848 distance: 93 - 94: 5.658 distance: 94 - 95: 6.250 distance: 94 - 97: 3.445 distance: 95 - 96: 30.992 distance: 95 - 100: 20.559 distance: 97 - 98: 11.502 distance: 97 - 99: 8.172 distance: 100 - 101: 14.945 distance: 101 - 102: 7.186 distance: 101 - 104: 17.758 distance: 102 - 103: 5.114 distance: 102 - 107: 4.761 distance: 104 - 105: 15.101 distance: 104 - 106: 11.477 distance: 111 - 112: 3.919 distance: 112 - 113: 3.776 distance: 118 - 119: 5.181 distance: 119 - 120: 4.291 distance: 119 - 122: 3.370 distance: 123 - 124: 3.219 distance: 124 - 125: 4.852 distance: 125 - 126: 6.911 distance: 129 - 130: 3.191 distance: 139 - 140: 3.438 distance: 140 - 141: 6.089 distance: 141 - 147: 4.301 distance: 144 - 146: 3.900 distance: 147 - 148: 3.534 distance: 149 - 150: 5.967 distance: 151 - 152: 3.743 distance: 152 - 153: 4.914 distance: 152 - 154: 4.396 distance: 156 - 157: 3.282 distance: 157 - 163: 4.743 distance: 159 - 160: 6.494 distance: 160 - 162: 4.632 distance: 166 - 195: 6.876 distance: 169 - 170: 3.965