Starting phenix.real_space_refine on Sun Aug 24 11:04:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zje_14746/08_2025/7zje_14746.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zje_14746/08_2025/7zje_14746.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zje_14746/08_2025/7zje_14746.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zje_14746/08_2025/7zje_14746.map" model { file = "/net/cci-nas-00/data/ceres_data/7zje_14746/08_2025/7zje_14746.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zje_14746/08_2025/7zje_14746.cif" } resolution = 3.12 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= 0.001 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 12656 2.51 5 N 3224 2.21 5 O 3292 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 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: 19284 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4821 Classifications: {'peptide': 595} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 17, 'TRANS': 577} Chain breaks: 3 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 4821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4821 Classifications: {'peptide': 595} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 17, 'TRANS': 577} Chain breaks: 3 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 4821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4821 Classifications: {'peptide': 595} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 17, 'TRANS': 577} Chain breaks: 3 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 4821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4821 Classifications: {'peptide': 595} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 17, 'TRANS': 577} Chain breaks: 3 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 35 Time building chain proxies: 4.85, per 1000 atoms: 0.25 Number of scatterers: 19284 At special positions: 0 Unit cell: (148.12, 148.12, 115.957, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 3292 8.00 N 3224 7.00 C 12656 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: 1.92 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 1.2 microseconds 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4496 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 4 sheets defined 66.6% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 76 through 82 removed outlier: 4.164A pdb=" N PHE A 81 " --> pdb=" O ASP A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 97 removed outlier: 3.605A pdb=" N THR A 93 " --> pdb=" O PRO A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 removed outlier: 3.958A pdb=" N ASP A 108 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.822A pdb=" N LYS A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 166 through 174 Processing helix chain 'A' and resid 176 through 186 Processing helix chain 'A' and resid 196 through 204 removed outlier: 3.712A pdb=" N GLN A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N HIS A 202 " --> pdb=" O PHE A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 248 through 257 Processing helix chain 'A' and resid 260 through 282 removed outlier: 3.694A pdb=" N ALA A 265 " --> pdb=" O PRO A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 308 through 316 Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 368 through 372 removed outlier: 3.549A pdb=" N MET A 372 " --> pdb=" O ARG A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 389 removed outlier: 3.766A pdb=" N LYS A 380 " --> pdb=" O GLU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 414 Processing helix chain 'A' and resid 430 through 459 Processing helix chain 'A' and resid 460 through 466 removed outlier: 3.608A pdb=" N SER A 466 " --> pdb=" O ILE A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 492 removed outlier: 3.581A pdb=" N LEU A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE A 491 " --> pdb=" O GLN A 487 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N MET A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 511 removed outlier: 3.689A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 518 removed outlier: 3.700A pdb=" N ARG A 517 " --> pdb=" O TYR A 514 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY A 518 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 537 removed outlier: 4.283A pdb=" N TYR A 525 " --> pdb=" O HIS A 521 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N MET A 528 " --> pdb=" O ILE A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 560 Processing helix chain 'A' and resid 597 through 606 removed outlier: 3.883A pdb=" N PHE A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 648 removed outlier: 3.880A pdb=" N THR A 648 " --> pdb=" O LEU A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 656 removed outlier: 3.766A pdb=" N ASN A 655 " --> pdb=" O HIS A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 673 removed outlier: 3.596A pdb=" N ASN A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 718 removed outlier: 3.721A pdb=" N THR A 718 " --> pdb=" O ALA A 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 82 removed outlier: 4.164A pdb=" N PHE B 81 " --> pdb=" O ASP B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 97 removed outlier: 3.606A pdb=" N THR B 93 " --> pdb=" O PRO B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 113 removed outlier: 3.958A pdb=" N ASP B 108 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR B 112 " --> pdb=" O ASP B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.822A pdb=" N LYS B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'B' and resid 144 through 146 No H-bonds generated for 'chain 'B' and resid 144 through 146' Processing helix chain 'B' and resid 166 through 174 Processing helix chain 'B' and resid 176 through 186 Processing helix chain 'B' and resid 196 through 204 removed outlier: 3.712A pdb=" N GLN B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N HIS B 202 " --> pdb=" O PHE B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 248 through 257 Processing helix chain 'B' and resid 260 through 282 removed outlier: 3.694A pdb=" N ALA B 265 " --> pdb=" O PRO B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 290 Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 308 through 316 Processing helix chain 'B' and resid 355 through 362 Processing helix chain 'B' and resid 368 through 372 removed outlier: 3.549A pdb=" N MET B 372 " --> pdb=" O ARG B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 389 removed outlier: 3.766A pdb=" N LYS B 380 " --> pdb=" O GLU B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 414 Processing helix chain 'B' and resid 430 through 459 Processing helix chain 'B' and resid 460 through 466 removed outlier: 3.609A pdb=" N SER B 466 " --> pdb=" O ILE B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 492 removed outlier: 3.583A pdb=" N LEU B 477 " --> pdb=" O GLU B 473 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE B 491 " --> pdb=" O GLN B 487 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N MET B 492 " --> pdb=" O VAL B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 511 removed outlier: 3.689A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 518 removed outlier: 3.701A pdb=" N ARG B 517 " --> pdb=" O TYR B 514 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLY B 518 " --> pdb=" O TYR B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 537 removed outlier: 4.284A pdb=" N TYR B 525 " --> pdb=" O HIS B 521 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N MET B 528 " --> pdb=" O ILE B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 560 Processing helix chain 'B' and resid 597 through 606 removed outlier: 3.884A pdb=" N PHE B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 648 removed outlier: 3.879A pdb=" N THR B 648 " --> pdb=" O LEU B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 656 removed outlier: 3.767A pdb=" N ASN B 655 " --> pdb=" O HIS B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 673 removed outlier: 3.596A pdb=" N ASN B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 718 removed outlier: 3.721A pdb=" N THR B 718 " --> pdb=" O ALA B 714 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 82 removed outlier: 4.164A pdb=" N PHE C 81 " --> pdb=" O ASP C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 97 removed outlier: 3.606A pdb=" N THR C 93 " --> pdb=" O PRO C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 113 removed outlier: 3.958A pdb=" N ASP C 108 " --> pdb=" O LYS C 104 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR C 111 " --> pdb=" O THR C 107 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR C 112 " --> pdb=" O ASP C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.822A pdb=" N LYS C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'C' and resid 144 through 146 No H-bonds generated for 'chain 'C' and resid 144 through 146' Processing helix chain 'C' and resid 166 through 174 Processing helix chain 'C' and resid 176 through 186 Processing helix chain 'C' and resid 196 through 204 removed outlier: 3.711A pdb=" N GLN C 200 " --> pdb=" O GLY C 196 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N HIS C 202 " --> pdb=" O PHE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 220 Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 248 through 257 Processing helix chain 'C' and resid 260 through 282 removed outlier: 3.693A pdb=" N ALA C 265 " --> pdb=" O PRO C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 290 Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 308 through 316 Processing helix chain 'C' and resid 355 through 362 Processing helix chain 'C' and resid 368 through 372 removed outlier: 3.548A pdb=" N MET C 372 " --> pdb=" O ARG C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 389 removed outlier: 3.766A pdb=" N LYS C 380 " --> pdb=" O GLU C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 414 Processing helix chain 'C' and resid 430 through 459 Processing helix chain 'C' and resid 460 through 466 removed outlier: 3.608A pdb=" N SER C 466 " --> pdb=" O ILE C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 492 removed outlier: 3.582A pdb=" N LEU C 477 " --> pdb=" O GLU C 473 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE C 491 " --> pdb=" O GLN C 487 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N MET C 492 " --> pdb=" O VAL C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 511 removed outlier: 3.689A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 518 removed outlier: 3.700A pdb=" N ARG C 517 " --> pdb=" O TYR C 514 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY C 518 " --> pdb=" O TYR C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 537 removed outlier: 4.284A pdb=" N TYR C 525 " --> pdb=" O HIS C 521 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N MET C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 560 Processing helix chain 'C' and resid 597 through 606 removed outlier: 3.883A pdb=" N PHE C 601 " --> pdb=" O SER C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 648 removed outlier: 3.879A pdb=" N THR C 648 " --> pdb=" O LEU C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 656 removed outlier: 3.767A pdb=" N ASN C 655 " --> pdb=" O HIS C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 673 removed outlier: 3.596A pdb=" N ASN C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 718 removed outlier: 3.721A pdb=" N THR C 718 " --> pdb=" O ALA C 714 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 82 removed outlier: 4.164A pdb=" N PHE D 81 " --> pdb=" O ASP D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 97 removed outlier: 3.606A pdb=" N THR D 93 " --> pdb=" O PRO D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 113 removed outlier: 3.958A pdb=" N ASP D 108 " --> pdb=" O LYS D 104 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR D 111 " --> pdb=" O THR D 107 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR D 112 " --> pdb=" O ASP D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.822A pdb=" N LYS D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 143 Processing helix chain 'D' and resid 144 through 146 No H-bonds generated for 'chain 'D' and resid 144 through 146' Processing helix chain 'D' and resid 166 through 174 Processing helix chain 'D' and resid 176 through 186 Processing helix chain 'D' and resid 196 through 204 removed outlier: 3.712A pdb=" N GLN D 200 " --> pdb=" O GLY D 196 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N HIS D 202 " --> pdb=" O PHE D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 220 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 248 through 257 Processing helix chain 'D' and resid 260 through 282 removed outlier: 3.693A pdb=" N ALA D 265 " --> pdb=" O PRO D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 290 Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 308 through 316 Processing helix chain 'D' and resid 355 through 362 Processing helix chain 'D' and resid 368 through 372 removed outlier: 3.549A pdb=" N MET D 372 " --> pdb=" O ARG D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 389 removed outlier: 3.766A pdb=" N LYS D 380 " --> pdb=" O GLU D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 414 Processing helix chain 'D' and resid 430 through 459 Processing helix chain 'D' and resid 460 through 466 removed outlier: 3.609A pdb=" N SER D 466 " --> pdb=" O ILE D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 492 removed outlier: 3.582A pdb=" N LEU D 477 " --> pdb=" O GLU D 473 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE D 491 " --> pdb=" O GLN D 487 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N MET D 492 " --> pdb=" O VAL D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 511 removed outlier: 3.689A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 518 removed outlier: 3.701A pdb=" N ARG D 517 " --> pdb=" O TYR D 514 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY D 518 " --> pdb=" O TYR D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 537 removed outlier: 4.284A pdb=" N TYR D 525 " --> pdb=" O HIS D 521 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N MET D 528 " --> pdb=" O ILE D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 560 Processing helix chain 'D' and resid 597 through 606 removed outlier: 3.884A pdb=" N PHE D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 648 removed outlier: 3.880A pdb=" N THR D 648 " --> pdb=" O LEU D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 651 through 656 removed outlier: 3.767A pdb=" N ASN D 655 " --> pdb=" O HIS D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 673 removed outlier: 3.596A pdb=" N ASN D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 718 removed outlier: 3.721A pdb=" N THR D 718 " --> pdb=" O ALA D 714 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 332 Processing sheet with id=AA2, first strand: chain 'B' and resid 329 through 332 Processing sheet with id=AA3, first strand: chain 'C' and resid 329 through 332 Processing sheet with id=AA4, first strand: chain 'D' and resid 329 through 332 1036 hydrogen bonds defined for protein. 2976 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.46 Time building geometry restraints manager: 2.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5996 1.35 - 1.46: 4844 1.46 - 1.58: 8748 1.58 - 1.70: 0 1.70 - 1.81: 172 Bond restraints: 19760 Sorted by residual: bond pdb=" N MET A 640 " pdb=" CA MET A 640 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.19e-02 7.06e+03 4.65e+00 bond pdb=" N MET D 640 " pdb=" CA MET D 640 " ideal model delta sigma weight residual 1.459 1.485 -0.025 1.19e-02 7.06e+03 4.59e+00 bond pdb=" N MET C 640 " pdb=" CA MET C 640 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.19e-02 7.06e+03 4.03e+00 bond pdb=" N MET B 640 " pdb=" CA MET B 640 " ideal model delta sigma weight residual 1.459 1.483 -0.023 1.19e-02 7.06e+03 3.89e+00 bond pdb=" C GLU A 376 " pdb=" N PRO A 377 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.20e-02 6.94e+03 2.37e+00 ... (remaining 19755 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 25887 1.29 - 2.58: 668 2.58 - 3.87: 171 3.87 - 5.16: 46 5.16 - 6.46: 32 Bond angle restraints: 26804 Sorted by residual: angle pdb=" CA GLU D 352 " pdb=" CB GLU D 352 " pdb=" CG GLU D 352 " ideal model delta sigma weight residual 114.10 120.51 -6.41 2.00e+00 2.50e-01 1.03e+01 angle pdb=" CA GLU C 352 " pdb=" CB GLU C 352 " pdb=" CG GLU C 352 " ideal model delta sigma weight residual 114.10 120.49 -6.39 2.00e+00 2.50e-01 1.02e+01 angle pdb=" CA GLU B 352 " pdb=" CB GLU B 352 " pdb=" CG GLU B 352 " ideal model delta sigma weight residual 114.10 120.48 -6.38 2.00e+00 2.50e-01 1.02e+01 angle pdb=" CA GLU A 352 " pdb=" CB GLU A 352 " pdb=" CG GLU A 352 " ideal model delta sigma weight residual 114.10 120.48 -6.38 2.00e+00 2.50e-01 1.02e+01 angle pdb=" C PHE D 519 " pdb=" N GLN D 520 " pdb=" CA GLN D 520 " ideal model delta sigma weight residual 120.82 124.97 -4.15 1.50e+00 4.44e-01 7.66e+00 ... (remaining 26799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.15: 10459 14.15 - 28.30: 731 28.30 - 42.45: 334 42.45 - 56.60: 44 56.60 - 70.74: 8 Dihedral angle restraints: 11576 sinusoidal: 4620 harmonic: 6956 Sorted by residual: dihedral pdb=" CA LEU A 345 " pdb=" C LEU A 345 " pdb=" N SER A 346 " pdb=" CA SER A 346 " ideal model delta harmonic sigma weight residual 180.00 161.95 18.05 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA LEU B 345 " pdb=" C LEU B 345 " pdb=" N SER B 346 " pdb=" CA SER B 346 " ideal model delta harmonic sigma weight residual 180.00 161.95 18.05 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA LEU D 345 " pdb=" C LEU D 345 " pdb=" N SER D 346 " pdb=" CA SER D 346 " ideal model delta harmonic sigma weight residual 180.00 161.97 18.03 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 11573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2070 0.033 - 0.066: 750 0.066 - 0.100: 192 0.100 - 0.133: 24 0.133 - 0.166: 8 Chirality restraints: 3044 Sorted by residual: chirality pdb=" CA MET A 640 " pdb=" N MET A 640 " pdb=" C MET A 640 " pdb=" CB MET A 640 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.90e-01 chirality pdb=" CA MET C 640 " pdb=" N MET C 640 " pdb=" C MET C 640 " pdb=" CB MET C 640 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA MET B 640 " pdb=" N MET B 640 " pdb=" C MET B 640 " pdb=" CB MET B 640 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.86e-01 ... (remaining 3041 not shown) Planarity restraints: 3292 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 148 " -0.032 5.00e-02 4.00e+02 4.86e-02 3.78e+00 pdb=" N PRO B 149 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 149 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 149 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 148 " -0.032 5.00e-02 4.00e+02 4.86e-02 3.78e+00 pdb=" N PRO C 149 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO C 149 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 149 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 148 " -0.032 5.00e-02 4.00e+02 4.85e-02 3.76e+00 pdb=" N PRO D 149 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO D 149 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 149 " -0.027 5.00e-02 4.00e+02 ... (remaining 3289 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4228 2.78 - 3.31: 19254 3.31 - 3.84: 30476 3.84 - 4.37: 33303 4.37 - 4.90: 59116 Nonbonded interactions: 146377 Sorted by model distance: nonbonded pdb=" O PRO A 89 " pdb=" OG1 THR A 93 " model vdw 2.254 3.040 nonbonded pdb=" O PRO D 89 " pdb=" OG1 THR D 93 " model vdw 2.255 3.040 nonbonded pdb=" O PRO C 89 " pdb=" OG1 THR C 93 " model vdw 2.255 3.040 nonbonded pdb=" O PRO B 89 " pdb=" OG1 THR B 93 " model vdw 2.255 3.040 nonbonded pdb=" OD1 ASP C 258 " pdb=" ND2 ASN C 263 " model vdw 2.292 3.120 ... (remaining 146372 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 4.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.860 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 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 : 0.002 0.038 19760 Z= 0.117 Angle : 0.574 6.455 26804 Z= 0.300 Chirality : 0.037 0.166 3044 Planarity : 0.004 0.049 3292 Dihedral : 11.987 70.744 7080 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.35 % Favored : 91.14 % Rotamer: Outliers : 0.19 % Allowed : 0.24 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.64 (0.18), residues: 2348 helix: 1.55 (0.14), residues: 1456 sheet: 2.42 (0.56), residues: 80 loop : -1.98 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 679 TYR 0.010 0.001 TYR A 271 PHE 0.014 0.001 PHE A 407 TRP 0.009 0.001 TRP A 223 HIS 0.005 0.001 HIS C 165 Details of bonding type rmsd covalent geometry : bond 0.00240 (19760) covalent geometry : angle 0.57359 (26804) hydrogen bonds : bond 0.14652 ( 1036) hydrogen bonds : angle 4.60963 ( 2976) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 308 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 536 ASP cc_start: 0.8653 (t70) cc_final: 0.8043 (t0) REVERT: B 536 ASP cc_start: 0.8661 (t70) cc_final: 0.8030 (t0) REVERT: C 536 ASP cc_start: 0.8685 (t70) cc_final: 0.8053 (t0) REVERT: D 536 ASP cc_start: 0.8702 (t70) cc_final: 0.8242 (t0) outliers start: 4 outliers final: 0 residues processed: 308 average time/residue: 0.1268 time to fit residues: 63.4004 Evaluate side-chains 262 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.4806 > 50: distance: 48 - 52: 7.740 distance: 52 - 53: 10.668 distance: 53 - 54: 4.004 distance: 53 - 56: 7.553 distance: 54 - 55: 29.949 distance: 54 - 60: 28.936 distance: 56 - 57: 8.286 distance: 57 - 58: 11.610 distance: 57 - 59: 16.601 distance: 60 - 61: 8.760 distance: 61 - 62: 22.091 distance: 62 - 63: 14.633 distance: 62 - 64: 11.207 distance: 64 - 65: 6.871 distance: 65 - 66: 4.457 distance: 66 - 67: 5.542 distance: 66 - 72: 3.641 distance: 68 - 69: 5.579 distance: 69 - 70: 6.706 distance: 69 - 71: 11.745 distance: 73 - 74: 5.029 distance: 73 - 76: 8.027 distance: 74 - 75: 10.492 distance: 75 - 104: 12.302 distance: 76 - 77: 14.137 distance: 76 - 78: 7.149 distance: 79 - 80: 10.004 distance: 80 - 81: 4.436 distance: 80 - 83: 8.543 distance: 81 - 82: 4.558 distance: 81 - 86: 11.845 distance: 82 - 109: 10.511 distance: 83 - 84: 5.196 distance: 83 - 85: 7.488 distance: 86 - 87: 8.543 distance: 88 - 89: 6.640 distance: 89 - 117: 8.123 distance: 90 - 91: 3.203 distance: 91 - 92: 5.883 distance: 95 - 96: 4.157 distance: 96 - 104: 3.976 distance: 97 - 124: 5.180 distance: 98 - 99: 7.768 distance: 99 - 101: 5.289 distance: 100 - 102: 3.402 distance: 101 - 103: 3.830 distance: 104 - 105: 3.253 distance: 105 - 106: 3.215 distance: 105 - 108: 4.055 distance: 106 - 107: 3.863 distance: 106 - 109: 5.964 distance: 109 - 110: 3.153 distance: 110 - 113: 8.670 distance: 111 - 112: 6.496 distance: 112 - 138: 11.396 distance: 113 - 114: 7.254 distance: 114 - 115: 8.812 distance: 114 - 116: 14.620 distance: 117 - 118: 5.544 distance: 118 - 119: 9.078 distance: 118 - 121: 6.899 distance: 119 - 120: 12.520 distance: 119 - 124: 7.770 distance: 121 - 122: 9.192 distance: 121 - 123: 6.175