Starting phenix.real_space_refine on Fri Jul 3 12:07:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e3q_47494/07_2026/9e3q_47494.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e3q_47494/07_2026/9e3q_47494.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e3q_47494/07_2026/9e3q_47494.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e3q_47494/07_2026/9e3q_47494.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e3q_47494/07_2026/9e3q_47494.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e3q_47494/07_2026/9e3q_47494.map" } resolution = 2.53 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= 0.019 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: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 6 5.49 5 S 102 5.16 5 Na 1 4.78 5 C 8568 2.51 5 N 2283 2.21 5 O 2656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13622 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4366 Classifications: {'peptide': 540} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 510} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 4366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4366 Classifications: {'peptide': 540} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 510} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 4366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4366 Classifications: {'peptide': 540} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 510} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 82 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {' ZN': 2, 'NAG': 2, 'PLM': 5} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PLM:plan-1': 5} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 82 Unusual residues: {' ZN': 2, 'NAG': 2, 'PLM': 5} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PLM:plan-1': 5} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 82 Unusual residues: {' ZN': 2, 'NAG': 2, 'PLM': 5} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PLM:plan-1': 5} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 65 Classifications: {'water': 65} Link IDs: {None: 64} Chain: "B" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 65 Classifications: {'water': 65} Link IDs: {None: 64} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3409 SG CYS A 479 20.303 50.263 15.427 1.00 49.44 S ATOM 3565 SG CYS A 499 23.312 51.328 17.437 1.00 40.42 S ATOM 3624 SG CYS A 506 23.712 49.633 13.976 1.00 48.36 S ATOM 4162 SG CYS A 572 22.634 47.632 17.000 1.00 37.32 S ATOM 3394 SG CYS A 477 16.714 49.773 16.234 1.00 47.57 S ATOM 3409 SG CYS A 479 20.303 50.263 15.427 1.00 49.44 S ATOM 3427 SG CYS A 482 19.189 47.366 17.765 1.00 44.55 S ATOM 3559 SG CYS A 498 19.260 50.973 18.934 1.00 38.29 S ATOM 7775 SG CYS B 479 59.234 18.772 15.685 1.00 49.44 S ATOM 7931 SG CYS B 499 56.804 20.862 17.673 1.00 40.42 S ATOM 7990 SG CYS B 506 58.076 22.025 14.203 1.00 48.36 S ATOM 8528 SG CYS B 572 60.344 22.121 17.230 1.00 37.32 S ATOM 7760 SG CYS B 477 61.453 15.917 16.521 1.00 47.57 S ATOM 7775 SG CYS B 479 59.234 18.772 15.685 1.00 49.44 S ATOM 7793 SG CYS B 482 62.297 19.278 18.023 1.00 44.55 S ATOM 7925 SG CYS B 498 59.137 17.545 19.203 1.00 38.29 S ATOM 12141 SG CYS C 479 67.022 68.221 15.501 1.00 49.44 S ATOM 12297 SG CYS C 499 66.425 65.089 17.517 1.00 40.42 S ATOM 12356 SG CYS C 506 64.785 65.577 14.041 1.00 48.36 S ATOM 12894 SG CYS C 572 63.566 67.521 17.048 1.00 37.32 S ATOM 12126 SG CYS C 477 68.384 71.577 16.307 1.00 47.57 S ATOM 12141 SG CYS C 479 67.022 68.221 15.501 1.00 49.44 S ATOM 12159 SG CYS C 482 65.050 70.641 17.814 1.00 44.55 S ATOM 12291 SG CYS C 498 68.129 68.782 19.015 1.00 38.29 S Time building chain proxies: 3.64, per 1000 atoms: 0.27 Number of scatterers: 13622 At special positions: 0 Unit cell: (92.016, 94.608, 161.352, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 102 16.00 P 6 15.00 Na 1 11.00 O 2656 8.00 N 2283 7.00 C 8568 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS A 216 " - pdb=" SG CYS A 226 " distance=2.04 Simple disulfide: pdb=" SG CYS A 260 " - pdb=" SG CYS A 269 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 168 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 226 " distance=2.04 Simple disulfide: pdb=" SG CYS B 260 " - pdb=" SG CYS B 269 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 168 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS C 216 " - pdb=" SG CYS C 226 " distance=2.04 Simple disulfide: pdb=" SG CYS C 260 " - pdb=" SG CYS C 269 " 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=15, symmetry=0 Links applied NAG-ASN " NAG A 704 " - " ASN A 187 " " NAG A 705 " - " ASN A 241 " " NAG B 704 " - " ASN B 187 " " NAG B 705 " - " ASN B 241 " " NAG C 704 " - " ASN C 187 " " NAG C 705 " - " ASN C 241 " Number of additional bonds: simple=15, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 733.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 702 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 499 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 506 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 572 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 479 " pdb=" ZN A 703 " pdb="ZN ZN A 703 " - pdb=" SG CYS A 479 " pdb="ZN ZN A 703 " - pdb=" SG CYS A 498 " pdb="ZN ZN A 703 " - pdb=" SG CYS A 482 " pdb="ZN ZN A 703 " - pdb=" SG CYS A 477 " pdb=" ZN B 702 " pdb="ZN ZN B 702 " - pdb=" SG CYS B 499 " pdb="ZN ZN B 702 " - pdb=" SG CYS B 506 " pdb="ZN ZN B 702 " - pdb=" SG CYS B 572 " pdb="ZN ZN B 702 " - pdb=" SG CYS B 479 " pdb=" ZN B 703 " pdb="ZN ZN B 703 " - pdb=" SG CYS B 479 " pdb="ZN ZN B 703 " - pdb=" SG CYS B 498 " pdb="ZN ZN B 703 " - pdb=" SG CYS B 482 " pdb="ZN ZN B 703 " - pdb=" SG CYS B 477 " pdb=" ZN C 702 " pdb="ZN ZN C 702 " - pdb=" SG CYS C 499 " pdb="ZN ZN C 702 " - pdb=" SG CYS C 506 " pdb="ZN ZN C 702 " - pdb=" SG CYS C 572 " pdb="ZN ZN C 702 " - pdb=" SG CYS C 479 " pdb=" ZN C 703 " pdb="ZN ZN C 703 " - pdb=" SG CYS C 479 " pdb="ZN ZN C 703 " - pdb=" SG CYS C 498 " pdb="ZN ZN C 703 " - pdb=" SG CYS C 482 " pdb="ZN ZN C 703 " - pdb=" SG CYS C 477 " Number of angles added : 36 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3048 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 21 sheets defined 36.4% alpha, 32.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 6 through 11 Processing helix chain 'A' and resid 23 through 48 Processing helix chain 'A' and resid 89 through 94 Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 231 through 238 Processing helix chain 'A' and resid 241 through 246 Processing helix chain 'A' and resid 263 through 267 removed outlier: 4.016A pdb=" N HIS A 267 " --> pdb=" O SER A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 288 Processing helix chain 'A' and resid 329 through 339 Processing helix chain 'A' and resid 340 through 344 Processing helix chain 'A' and resid 345 through 358 Processing helix chain 'A' and resid 361 through 367 Processing helix chain 'A' and resid 371 through 377 removed outlier: 3.762A pdb=" N CYS A 374 " --> pdb=" O CYS A 371 " (cutoff:3.500A) Proline residue: A 376 - end of helix Processing helix chain 'A' and resid 378 through 387 removed outlier: 4.014A pdb=" N TYR A 382 " --> pdb=" O THR A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 490 No H-bonds generated for 'chain 'A' and resid 488 through 490' Processing helix chain 'A' and resid 491 through 496 removed outlier: 4.322A pdb=" N GLU A 495 " --> pdb=" O ARG A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 509 Processing helix chain 'A' and resid 510 through 517 removed outlier: 3.900A pdb=" N HIS A 514 " --> pdb=" O SER A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 531 Processing helix chain 'A' and resid 537 through 559 Processing helix chain 'A' and resid 560 through 565 Processing helix chain 'A' and resid 570 through 581 Processing helix chain 'B' and resid 7 through 11 Processing helix chain 'B' and resid 23 through 48 Processing helix chain 'B' and resid 89 through 94 Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 231 through 238 Processing helix chain 'B' and resid 241 through 246 Processing helix chain 'B' and resid 263 through 267 removed outlier: 4.016A pdb=" N HIS B 267 " --> pdb=" O SER B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 288 Processing helix chain 'B' and resid 329 through 339 Processing helix chain 'B' and resid 340 through 344 Processing helix chain 'B' and resid 345 through 358 Processing helix chain 'B' and resid 361 through 367 Processing helix chain 'B' and resid 371 through 377 removed outlier: 3.762A pdb=" N CYS B 374 " --> pdb=" O CYS B 371 " (cutoff:3.500A) Proline residue: B 376 - end of helix Processing helix chain 'B' and resid 378 through 387 removed outlier: 4.014A pdb=" N TYR B 382 " --> pdb=" O THR B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 490 No H-bonds generated for 'chain 'B' and resid 488 through 490' Processing helix chain 'B' and resid 491 through 496 removed outlier: 4.322A pdb=" N GLU B 495 " --> pdb=" O ARG B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 509 Processing helix chain 'B' and resid 510 through 517 removed outlier: 3.900A pdb=" N HIS B 514 " --> pdb=" O SER B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 531 Processing helix chain 'B' and resid 537 through 559 Processing helix chain 'B' and resid 560 through 565 Processing helix chain 'B' and resid 570 through 581 Processing helix chain 'C' and resid 7 through 11 Processing helix chain 'C' and resid 23 through 48 Processing helix chain 'C' and resid 89 through 94 Processing helix chain 'C' and resid 182 through 187 Processing helix chain 'C' and resid 231 through 238 Processing helix chain 'C' and resid 241 through 246 Processing helix chain 'C' and resid 263 through 267 removed outlier: 4.016A pdb=" N HIS C 267 " --> pdb=" O SER C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 288 Processing helix chain 'C' and resid 329 through 339 Processing helix chain 'C' and resid 340 through 344 Processing helix chain 'C' and resid 345 through 358 Processing helix chain 'C' and resid 361 through 367 Processing helix chain 'C' and resid 371 through 377 removed outlier: 3.761A pdb=" N CYS C 374 " --> pdb=" O CYS C 371 " (cutoff:3.500A) Proline residue: C 376 - end of helix Processing helix chain 'C' and resid 378 through 387 removed outlier: 4.014A pdb=" N TYR C 382 " --> pdb=" O THR C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 490 No H-bonds generated for 'chain 'C' and resid 488 through 490' Processing helix chain 'C' and resid 491 through 496 removed outlier: 4.322A pdb=" N GLU C 495 " --> pdb=" O ARG C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 509 Processing helix chain 'C' and resid 510 through 517 removed outlier: 3.901A pdb=" N HIS C 514 " --> pdb=" O SER C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 531 Processing helix chain 'C' and resid 537 through 559 Processing helix chain 'C' and resid 560 through 565 Processing helix chain 'C' and resid 570 through 581 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 16 Processing sheet with id=AA2, first strand: chain 'B' and resid 13 through 16 removed outlier: 6.608A pdb=" N VAL A 18 " --> pdb=" O GLU C 389 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ILE C 391 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ARG A 20 " --> pdb=" O ILE C 391 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 137 through 140 removed outlier: 5.261A pdb=" N GLN A 148 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N ILE A 147 " --> pdb=" O TRP A 167 " (cutoff:3.500A) removed outlier: 9.121A pdb=" N TRP A 167 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N THR A 149 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N SER A 165 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ARG A 151 " --> pdb=" O GLU A 163 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N PHE A 313 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N TYR A 108 " --> pdb=" O LYS A 311 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LYS A 311 " --> pdb=" O TYR A 108 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LYS A 110 " --> pdb=" O LEU A 309 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU A 309 " --> pdb=" O LYS A 110 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLU A 112 " --> pdb=" O ARG A 307 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ARG A 307 " --> pdb=" O GLU A 112 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLN A 114 " --> pdb=" O GLU A 305 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLU A 305 " --> pdb=" O GLN A 114 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 58 through 66 Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 66 Processing sheet with id=AA7, first strand: chain 'A' and resid 69 through 71 Processing sheet with id=AA8, first strand: chain 'A' and resid 388 through 392 Processing sheet with id=AA9, first strand: chain 'A' and resid 400 through 402 Processing sheet with id=AB1, first strand: chain 'B' and resid 52 through 56 Processing sheet with id=AB2, first strand: chain 'B' and resid 137 through 140 removed outlier: 5.261A pdb=" N GLN B 148 " --> pdb=" O GLY B 138 " (cutoff:3.500A) removed outlier: 9.216A pdb=" N ILE B 147 " --> pdb=" O TRP B 167 " (cutoff:3.500A) removed outlier: 9.121A pdb=" N TRP B 167 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N THR B 149 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N SER B 165 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ARG B 151 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N PHE B 313 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TYR B 108 " --> pdb=" O LYS B 311 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LYS B 311 " --> pdb=" O TYR B 108 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LYS B 110 " --> pdb=" O LEU B 309 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU B 309 " --> pdb=" O LYS B 110 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLU B 112 " --> pdb=" O ARG B 307 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ARG B 307 " --> pdb=" O GLU B 112 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLN B 114 " --> pdb=" O GLU B 305 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLU B 305 " --> pdb=" O GLN B 114 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 58 through 66 Processing sheet with id=AB4, first strand: chain 'B' and resid 58 through 66 Processing sheet with id=AB5, first strand: chain 'B' and resid 69 through 71 Processing sheet with id=AB6, first strand: chain 'B' and resid 400 through 402 Processing sheet with id=AB7, first strand: chain 'C' and resid 52 through 56 Processing sheet with id=AB8, first strand: chain 'C' and resid 137 through 140 removed outlier: 5.261A pdb=" N GLN C 148 " --> pdb=" O GLY C 138 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N ILE C 147 " --> pdb=" O TRP C 167 " (cutoff:3.500A) removed outlier: 9.121A pdb=" N TRP C 167 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N THR C 149 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N SER C 165 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ARG C 151 " --> pdb=" O GLU C 163 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N PHE C 313 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TYR C 108 " --> pdb=" O LYS C 311 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LYS C 311 " --> pdb=" O TYR C 108 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LYS C 110 " --> pdb=" O LEU C 309 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU C 309 " --> pdb=" O LYS C 110 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLU C 112 " --> pdb=" O ARG C 307 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ARG C 307 " --> pdb=" O GLU C 112 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLN C 114 " --> pdb=" O GLU C 305 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLU C 305 " --> pdb=" O GLN C 114 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 58 through 66 Processing sheet with id=AC1, first strand: chain 'C' and resid 58 through 66 Processing sheet with id=AC2, first strand: chain 'C' and resid 69 through 71 Processing sheet with id=AC3, first strand: chain 'C' and resid 400 through 402 594 hydrogen bonds defined for protein. 1593 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.27 Time building geometry restraints manager: 1.62 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: 4225 1.34 - 1.46: 3354 1.46 - 1.58: 6041 1.58 - 1.70: 9 1.70 - 1.82: 126 Bond restraints: 13755 Sorted by residual: bond pdb=" N ASN C 107 " pdb=" CA ASN C 107 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.27e-02 6.20e+03 6.50e+00 bond pdb=" N ASN A 107 " pdb=" CA ASN A 107 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.27e-02 6.20e+03 6.37e+00 bond pdb=" N ASP A 413 " pdb=" CA ASP A 413 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.32e-02 5.74e+03 6.35e+00 bond pdb=" N ASN B 107 " pdb=" CA ASN B 107 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.27e-02 6.20e+03 6.25e+00 bond pdb=" N ASP B 413 " pdb=" CA ASP B 413 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.32e-02 5.74e+03 6.25e+00 ... (remaining 13750 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 17686 1.38 - 2.76: 658 2.76 - 4.13: 169 4.13 - 5.51: 45 5.51 - 6.89: 24 Bond angle restraints: 18582 Sorted by residual: angle pdb=" CA CYS A 373 " pdb=" C CYS A 373 " pdb=" O CYS A 373 " ideal model delta sigma weight residual 119.31 124.36 -5.05 1.24e+00 6.50e-01 1.66e+01 angle pdb=" CA CYS B 373 " pdb=" C CYS B 373 " pdb=" O CYS B 373 " ideal model delta sigma weight residual 119.31 124.33 -5.02 1.24e+00 6.50e-01 1.64e+01 angle pdb=" CA CYS C 373 " pdb=" C CYS C 373 " pdb=" O CYS C 373 " ideal model delta sigma weight residual 119.31 124.32 -5.01 1.24e+00 6.50e-01 1.63e+01 angle pdb=" CA CYS B 374 " pdb=" C CYS B 374 " pdb=" O CYS B 374 " ideal model delta sigma weight residual 119.43 124.06 -4.63 1.21e+00 6.83e-01 1.46e+01 angle pdb=" CA CYS A 374 " pdb=" C CYS A 374 " pdb=" O CYS A 374 " ideal model delta sigma weight residual 119.43 124.03 -4.60 1.21e+00 6.83e-01 1.45e+01 ... (remaining 18577 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.57: 7649 22.57 - 45.14: 561 45.14 - 67.71: 103 67.71 - 90.29: 18 90.29 - 112.86: 3 Dihedral angle restraints: 8334 sinusoidal: 3585 harmonic: 4749 Sorted by residual: dihedral pdb=" C5' GDP B 701 " pdb=" O5' GDP B 701 " pdb=" PA GDP B 701 " pdb=" O3A GDP B 701 " ideal model delta sinusoidal sigma weight residual 179.98 67.12 112.86 1 2.00e+01 2.50e-03 3.33e+01 dihedral pdb=" C5' GDP A 701 " pdb=" O5' GDP A 701 " pdb=" PA GDP A 701 " pdb=" O3A GDP A 701 " ideal model delta sinusoidal sigma weight residual 179.98 67.15 112.83 1 2.00e+01 2.50e-03 3.33e+01 dihedral pdb=" C5' GDP C 701 " pdb=" O5' GDP C 701 " pdb=" PA GDP C 701 " pdb=" O3A GDP C 701 " ideal model delta sinusoidal sigma weight residual 179.98 67.15 112.83 1 2.00e+01 2.50e-03 3.33e+01 ... (remaining 8331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1299 0.037 - 0.075: 479 0.075 - 0.112: 156 0.112 - 0.150: 40 0.150 - 0.187: 6 Chirality restraints: 1980 Sorted by residual: chirality pdb=" CA ARG C 53 " pdb=" N ARG C 53 " pdb=" C ARG C 53 " pdb=" CB ARG C 53 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.74e-01 chirality pdb=" CA ARG B 53 " pdb=" N ARG B 53 " pdb=" C ARG B 53 " pdb=" CB ARG B 53 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.59e-01 chirality pdb=" CA ARG A 53 " pdb=" N ARG A 53 " pdb=" C ARG A 53 " pdb=" CB ARG A 53 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.18 2.00e-01 2.50e+01 8.55e-01 ... (remaining 1977 not shown) Planarity restraints: 2346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 241 " 0.079 2.00e-02 2.50e+03 9.29e-02 1.08e+02 pdb=" CG ASN B 241 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN B 241 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN B 241 " -0.153 2.00e-02 2.50e+03 pdb=" C1 NAG B 705 " 0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 241 " 0.079 2.00e-02 2.50e+03 9.27e-02 1.07e+02 pdb=" CG ASN A 241 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN A 241 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 241 " -0.153 2.00e-02 2.50e+03 pdb=" C1 NAG A 705 " 0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 241 " 0.079 2.00e-02 2.50e+03 9.25e-02 1.07e+02 pdb=" CG ASN C 241 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN C 241 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN C 241 " -0.152 2.00e-02 2.50e+03 pdb=" C1 NAG C 705 " 0.111 2.00e-02 2.50e+03 ... (remaining 2343 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2153 2.76 - 3.30: 12112 3.30 - 3.83: 24015 3.83 - 4.37: 30349 4.37 - 4.90: 49253 Nonbonded interactions: 117882 Sorted by model distance: nonbonded pdb=" O CYS B 269 " pdb=" O HOH B 801 " model vdw 2.227 3.040 nonbonded pdb=" O CYS A 269 " pdb=" O HOH A 801 " model vdw 2.236 3.040 nonbonded pdb=" O CYS C 269 " pdb=" O HOH C 801 " model vdw 2.246 3.040 nonbonded pdb=" O ASP C 259 " pdb=" O HOH C 802 " model vdw 2.265 3.040 nonbonded pdb=" OG SER A 274 " pdb=" O HOH A 802 " model vdw 2.267 3.040 ... (remaining 117877 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 6 through 710) selection = chain 'B' selection = chain 'C' } 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: 24.880 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: 0.030 Extract box with map and model: 0.340 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.270 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 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 : 0.005 0.044 13815 Z= 0.273 Angle : 0.718 8.237 18666 Z= 0.393 Chirality : 0.045 0.187 1980 Planarity : 0.006 0.101 2340 Dihedral : 15.769 112.858 5241 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.41 % Allowed : 14.29 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 are not related in a simple way. whole: 0.81 (0.21), residues: 1602 helix: 0.20 (0.24), residues: 444 sheet: 0.23 (0.26), residues: 360 loop : 1.15 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 307 TYR 0.010 0.001 TYR C 336 PHE 0.014 0.002 PHE C 275 TRP 0.013 0.002 TRP C 575 HIS 0.003 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.25 (13755) covalent geometry : angle 0.69633 / 0.39 (18582) SS BOND : bond 0.00250 / 0.15 ( 15) SS BOND : angle 0.93924 / 0.73 ( 30) hydrogen bonds : bond 0.19238 / 13.04 ( 564) hydrogen bonds : angle 7.87988 / 5.46 ( 1593) metal coordination : bond 0.00358 / 0.20 ( 24) metal coordination : angle 2.55277 / 1.68 ( 36) Misc. bond : bond 0.03510 / 2.13 ( 15) link_NAG-ASN : bond 0.02649 / 1.48 ( 6) link_NAG-ASN : angle 4.45059 / 2.83 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 150 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 551 ARG cc_start: 0.7892 (mtp180) cc_final: 0.7688 (mtt180) REVERT: A 592 LYS cc_start: 0.7955 (pttt) cc_final: 0.7306 (ptmm) REVERT: B 592 LYS cc_start: 0.7896 (pttt) cc_final: 0.7261 (ptmm) REVERT: C 592 LYS cc_start: 0.7956 (pttt) cc_final: 0.7284 (ptmm) outliers start: 6 outliers final: 5 residues processed: 156 average time/residue: 0.7283 time to fit residues: 122.6949 Evaluate side-chains 126 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 121 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain C residue 363 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 GLN A 85 HIS A 100 ASN A 408 HIS ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 HIS B 100 ASN C 22 GLN C 85 HIS C 100 ASN C 408 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.154706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.113326 restraints weight = 11794.100| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.51 r_work: 0.2922 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13815 Z= 0.147 Angle : 0.560 6.080 18666 Z= 0.277 Chirality : 0.043 0.135 1980 Planarity : 0.005 0.046 2340 Dihedral : 7.807 117.737 2066 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.07 % Allowed : 14.98 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 are not related in a simple way. whole: 1.24 (0.21), residues: 1602 helix: 1.09 (0.25), residues: 432 sheet: 0.16 (0.26), residues: 363 loop : 1.24 (0.23), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 544 TYR 0.011 0.001 TYR C 336 PHE 0.015 0.002 PHE C 275 TRP 0.012 0.002 TRP C 575 HIS 0.003 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (13755) covalent geometry : angle 0.53465 / 0.27 (18582) SS BOND : bond 0.00324 / 0.19 ( 15) SS BOND : angle 1.00245 / 0.77 ( 30) hydrogen bonds : bond 0.04203 / 2.85 ( 564) hydrogen bonds : angle 5.45827 / 3.69 ( 1593) metal coordination : bond 0.00357 / 0.21 ( 24) metal coordination : angle 3.05673 / 2.13 ( 36) Misc. bond : bond 0.00064 / 0.04 ( 15) link_NAG-ASN : bond 0.00196 / 0.11 ( 6) link_NAG-ASN : angle 3.02948 / 1.92 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 THR cc_start: 0.8605 (OUTLIER) cc_final: 0.8386 (t) REVERT: A 385 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7416 (mtp180) REVERT: A 592 LYS cc_start: 0.7909 (pttt) cc_final: 0.7068 (ptmm) REVERT: B 143 GLN cc_start: 0.7238 (OUTLIER) cc_final: 0.6879 (mm-40) REVERT: B 217 THR cc_start: 0.8606 (OUTLIER) cc_final: 0.8343 (t) REVERT: B 284 ASP cc_start: 0.7891 (t0) cc_final: 0.7656 (t70) REVERT: B 385 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7461 (mtp180) REVERT: B 592 LYS cc_start: 0.7858 (pttt) cc_final: 0.7022 (ptmm) REVERT: C 174 LYS cc_start: 0.7150 (OUTLIER) cc_final: 0.6929 (mtpt) REVERT: C 385 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7476 (ttm110) outliers start: 30 outliers final: 11 residues processed: 151 average time/residue: 0.7232 time to fit residues: 117.8447 Evaluate side-chains 147 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain A residue 385 ARG Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 385 ARG Chi-restraints excluded: chain C residue 525 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 60 optimal weight: 0.7980 chunk 40 optimal weight: 0.0270 chunk 119 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 ASN A 408 HIS B 100 ASN C 100 ASN C 408 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.155272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.105694 restraints weight = 11946.687| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.56 r_work: 0.3003 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13815 Z= 0.130 Angle : 0.527 6.351 18666 Z= 0.260 Chirality : 0.043 0.134 1980 Planarity : 0.004 0.047 2340 Dihedral : 7.451 115.764 2064 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 2.35 % Allowed : 15.46 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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 are not related in a simple way. whole: 1.36 (0.21), residues: 1602 helix: 1.36 (0.26), residues: 432 sheet: 0.16 (0.26), residues: 363 loop : 1.25 (0.23), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 20 TYR 0.011 0.001 TYR C 336 PHE 0.013 0.002 PHE C 275 TRP 0.012 0.001 TRP A 575 HIS 0.003 0.001 HIS B 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (13755) covalent geometry : angle 0.50498 / 0.26 (18582) SS BOND : bond 0.00334 / 0.20 ( 15) SS BOND : angle 1.02092 / 0.78 ( 30) hydrogen bonds : bond 0.03664 / 2.47 ( 564) hydrogen bonds : angle 5.11017 / 3.44 ( 1593) metal coordination : bond 0.00325 / 0.19 ( 24) metal coordination : angle 2.89367 / 1.99 ( 36) Misc. bond : bond 0.00023 / 0.01 ( 15) link_NAG-ASN : bond 0.00121 / 0.07 ( 6) link_NAG-ASN : angle 2.52323 / 1.59 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: A 284 ASP cc_start: 0.7746 (t0) cc_final: 0.7521 (t0) REVERT: A 385 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7259 (mtp180) REVERT: A 511 LYS cc_start: 0.6469 (OUTLIER) cc_final: 0.6134 (ptmm) REVERT: B 143 GLN cc_start: 0.7273 (OUTLIER) cc_final: 0.6910 (mm-40) REVERT: B 174 LYS cc_start: 0.7277 (OUTLIER) cc_final: 0.7032 (ptmt) REVERT: B 217 THR cc_start: 0.8508 (OUTLIER) cc_final: 0.8295 (t) REVERT: B 284 ASP cc_start: 0.7684 (t0) cc_final: 0.7403 (t0) REVERT: B 511 LYS cc_start: 0.6567 (OUTLIER) cc_final: 0.6239 (ptmm) REVERT: B 579 LYS cc_start: 0.8265 (ptmt) cc_final: 0.7528 (ptpp) REVERT: B 592 LYS cc_start: 0.7798 (pttt) cc_final: 0.6986 (ptmm) REVERT: C 174 LYS cc_start: 0.7118 (OUTLIER) cc_final: 0.6889 (mtpt) REVERT: C 217 THR cc_start: 0.8602 (OUTLIER) cc_final: 0.8357 (t) REVERT: C 284 ASP cc_start: 0.7793 (t70) cc_final: 0.7572 (t0) REVERT: C 305 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6773 (tm-30) REVERT: C 385 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7385 (ttm110) REVERT: C 392 MET cc_start: 0.8491 (mmm) cc_final: 0.8259 (tpp) outliers start: 34 outliers final: 11 residues processed: 153 average time/residue: 0.7714 time to fit residues: 127.1654 Evaluate side-chains 153 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 363 CYS Chi-restraints excluded: chain A residue 385 ARG Chi-restraints excluded: chain A residue 511 LYS Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain B residue 511 LYS Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 174 LYS Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 385 ARG Chi-restraints excluded: chain C residue 525 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.2584 > 50: distance: 8 - 37: 31.788 distance: 12 - 46: 36.060 distance: 20 - 54: 27.040 distance: 29 - 37: 34.846 distance: 38 - 39: 37.638 distance: 38 - 41: 40.237 distance: 39 - 40: 53.428 distance: 39 - 46: 3.103 distance: 42 - 43: 40.468 distance: 44 - 45: 41.062 distance: 46 - 47: 39.642 distance: 48 - 49: 40.895 distance: 48 - 54: 14.174 distance: 50 - 51: 55.785 distance: 51 - 52: 37.543 distance: 51 - 53: 4.193 distance: 54 - 55: 26.913 distance: 55 - 58: 40.108 distance: 56 - 57: 34.288 distance: 56 - 61: 41.808 distance: 58 - 60: 41.210 distance: 61 - 62: 16.029 distance: 62 - 63: 40.226 distance: 66 - 68: 39.811 distance: 69 - 70: 38.977 distance: 70 - 71: 56.699 distance: 70 - 73: 40.145 distance: 71 - 75: 44.456 distance: 72 - 101: 20.114 distance: 73 - 74: 57.128 distance: 76 - 77: 44.840 distance: 76 - 79: 43.698 distance: 77 - 86: 56.157 distance: 78 - 109: 57.561 distance: 79 - 80: 69.377 distance: 80 - 81: 64.380 distance: 81 - 82: 25.563 distance: 82 - 83: 30.721 distance: 83 - 84: 23.500 distance: 83 - 85: 18.455 distance: 86 - 87: 44.335 distance: 87 - 88: 17.932 distance: 87 - 90: 42.446 distance: 88 - 89: 39.654 distance: 88 - 94: 39.868 distance: 89 - 118: 34.480 distance: 90 - 91: 6.116 distance: 91 - 92: 57.387 distance: 91 - 93: 5.739 distance: 94 - 95: 40.578 distance: 95 - 96: 41.106 distance: 95 - 98: 39.131 distance: 96 - 97: 39.024 distance: 96 - 101: 22.939 distance: 97 - 126: 35.104 distance: 98 - 100: 40.008 distance: 101 - 102: 30.956 distance: 102 - 103: 20.675 distance: 102 - 105: 45.166 distance: 104 - 134: 35.160 distance: 105 - 106: 39.885 distance: 109 - 110: 40.217 distance: 110 - 111: 69.409 distance: 110 - 113: 40.403 distance: 111 - 112: 52.580 distance: 111 - 118: 33.538 distance: 112 - 142: 23.431 distance: 113 - 114: 4.840 distance: 115 - 117: 40.667