Starting phenix.real_space_refine on Sun Aug 24 08:31:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ue9_20751/08_2025/6ue9_20751.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ue9_20751/08_2025/6ue9_20751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ue9_20751/08_2025/6ue9_20751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ue9_20751/08_2025/6ue9_20751.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ue9_20751/08_2025/6ue9_20751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ue9_20751/08_2025/6ue9_20751.map" } resolution = 2.9 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= -0.013 sd= 0.420 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 98 5.16 5 C 11488 2.51 5 N 3151 2.21 5 O 3490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18227 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1616 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 18, 'TRANS': 202} Chain breaks: 2 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1686 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 18, 'TRANS': 212} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 6, 'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 52 Chain: "C" Number of atoms: 4150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4150 Classifications: {'peptide': 537} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 511} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1038 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 123} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1656 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 18, 'TRANS': 212} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 8, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 72 Chain: "G" Number of atoms: 1666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1666 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 18, 'TRANS': 212} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 8, 'ASP:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 64 Chain: "E" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1570 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 17, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 11, 'ASP:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 107 Chain: "H" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1556 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 18, 'TRANS': 205} Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 11, 'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 103 Chain: "K" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1581 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 18, 'TRANS': 202} Chain breaks: 2 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 8, 'ASP:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 74 Chain: "L" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1543 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 18, 'TRANS': 201} Chain breaks: 1 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 10, 'ASP:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 98 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.41, per 1000 atoms: 0.30 Number of scatterers: 18227 At special positions: 0 Unit cell: (173.196, 148.745, 174.215, 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 98 16.00 O 3490 8.00 N 3151 7.00 C 11488 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 242 " - pdb=" SG CYS B 299 " distance=2.04 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 323 " distance=2.04 Simple disulfide: pdb=" SG CYS A 299 " - pdb=" SG CYS B 242 " distance=2.05 Simple disulfide: pdb=" SG CYS A 369 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 323 " distance=2.04 Simple disulfide: pdb=" SG CYS B 369 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS D 69 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 202 " distance=2.03 Simple disulfide: pdb=" SG CYS C 239 " - pdb=" SG CYS C 307 " distance=2.03 Simple disulfide: pdb=" SG CYS C 253 " - pdb=" SG CYS C 261 " distance=2.04 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 377 " distance=2.04 Simple disulfide: pdb=" SG CYS C 464 " - pdb=" SG CYS C 526 " distance=2.04 Simple disulfide: pdb=" SG CYS C 468 " - pdb=" SG CYS F 311 " distance=2.04 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 485 " distance=2.04 Simple disulfide: pdb=" SG CYS D 13 " - pdb=" SG CYS D 101 " distance=2.04 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS F 471 " distance=2.02 Simple disulfide: pdb=" SG CYS D 72 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 109 " - pdb=" SG CYS D 134 " distance=2.05 Simple disulfide: pdb=" SG CYS F 242 " - pdb=" SG CYS G 299 " distance=2.04 Simple disulfide: pdb=" SG CYS F 266 " - pdb=" SG CYS F 323 " distance=2.04 Simple disulfide: pdb=" SG CYS F 299 " - pdb=" SG CYS G 242 " distance=2.03 Simple disulfide: pdb=" SG CYS F 369 " - pdb=" SG CYS F 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 266 " - pdb=" SG CYS G 323 " distance=2.04 Simple disulfide: pdb=" SG CYS G 369 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 471 " - pdb=" SG CYS E 471 " distance=2.03 Simple disulfide: pdb=" SG CYS E 242 " - pdb=" SG CYS H 299 " distance=2.04 Simple disulfide: pdb=" SG CYS E 299 " - pdb=" SG CYS H 242 " distance=2.03 Simple disulfide: pdb=" SG CYS E 369 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS H 266 " - pdb=" SG CYS H 323 " distance=2.04 Simple disulfide: pdb=" SG CYS H 369 " - pdb=" SG CYS H 432 " distance=2.03 Simple disulfide: pdb=" SG CYS K 242 " - pdb=" SG CYS L 299 " distance=2.04 Simple disulfide: pdb=" SG CYS K 266 " - pdb=" SG CYS K 323 " distance=2.04 Simple disulfide: pdb=" SG CYS K 299 " - pdb=" SG CYS L 242 " distance=2.04 Simple disulfide: pdb=" SG CYS K 369 " - pdb=" SG CYS K 432 " distance=2.03 Simple disulfide: pdb=" SG CYS L 266 " - pdb=" SG CYS L 323 " distance=2.04 Simple disulfide: pdb=" SG CYS L 369 " - pdb=" SG CYS L 432 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG A 501 " - " ASN A 337 " " NAG B 501 " - " ASN B 337 " " NAG C 601 " - " ASN C 403 " " NAG C 604 " - " ASN C 65 " " NAG C 605 " - " ASN C 451 " " NAG F 501 " - " ASN F 337 " " NAG G 501 " - " ASN G 337 " " NAG I 1 " - " ASN C 72 " " NAG J 1 " - " ASN D 49 " Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 947.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4598 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 55 sheets defined 9.7% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 252 through 258 removed outlier: 3.616A pdb=" N LEU A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.828A pdb=" N ASN A 316 " --> pdb=" O ALA A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 395 removed outlier: 3.759A pdb=" N TYR A 395 " --> pdb=" O ARG A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 427 removed outlier: 3.611A pdb=" N GLY A 427 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 258 removed outlier: 3.608A pdb=" N LEU B 256 " --> pdb=" O ALA B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 318 Processing helix chain 'B' and resid 355 through 359 removed outlier: 3.603A pdb=" N GLU B 358 " --> pdb=" O PRO B 355 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 359 " --> pdb=" O SER B 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 355 through 359' Processing helix chain 'B' and resid 391 through 393 No H-bonds generated for 'chain 'B' and resid 391 through 393' Processing helix chain 'B' and resid 421 through 427 removed outlier: 3.741A pdb=" N LYS B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY B 427 " --> pdb=" O ASP B 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 33 removed outlier: 3.652A pdb=" N HIS C 32 " --> pdb=" O SER C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 246 removed outlier: 3.777A pdb=" N VAL C 245 " --> pdb=" O GLY C 242 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA C 246 " --> pdb=" O PRO C 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 242 through 246' Processing helix chain 'C' and resid 272 through 276 removed outlier: 3.691A pdb=" N PHE C 275 " --> pdb=" O ALA C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 302 removed outlier: 3.775A pdb=" N ASP C 301 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA C 302 " --> pdb=" O LYS C 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 298 through 302' Processing helix chain 'C' and resid 356 through 360 removed outlier: 3.631A pdb=" N SER C 360 " --> pdb=" O ARG C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 418 removed outlier: 3.535A pdb=" N ASP C 417 " --> pdb=" O THR C 414 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA C 418 " --> pdb=" O SER C 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 414 through 418' Processing helix chain 'C' and resid 467 through 471 removed outlier: 3.637A pdb=" N SER C 471 " --> pdb=" O CYS C 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 69 Processing helix chain 'F' and resid 252 through 258 removed outlier: 3.661A pdb=" N LEU F 258 " --> pdb=" O GLU F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 318 removed outlier: 3.587A pdb=" N GLY F 318 " --> pdb=" O PRO F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 359 Processing helix chain 'F' and resid 391 through 393 No H-bonds generated for 'chain 'F' and resid 391 through 393' Processing helix chain 'F' and resid 421 through 427 removed outlier: 3.698A pdb=" N LYS F 425 " --> pdb=" O ALA F 421 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 258 removed outlier: 3.548A pdb=" N LEU G 258 " --> pdb=" O GLU G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 301 removed outlier: 4.320A pdb=" N GLY G 300 " --> pdb=" O ASP G 297 " (cutoff:3.500A) Processing helix chain 'G' and resid 355 through 360 Processing helix chain 'G' and resid 420 through 427 removed outlier: 3.615A pdb=" N GLY G 427 " --> pdb=" O ASP G 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 317 removed outlier: 3.697A pdb=" N ASN E 316 " --> pdb=" O GLN E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 360 removed outlier: 3.522A pdb=" N ALA E 360 " --> pdb=" O GLU E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 427 Processing helix chain 'H' and resid 252 through 258 removed outlier: 3.763A pdb=" N LEU H 258 " --> pdb=" O GLU H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 312 through 317 removed outlier: 3.552A pdb=" N ASN H 316 " --> pdb=" O ALA H 312 " (cutoff:3.500A) Processing helix chain 'H' and resid 357 through 362 removed outlier: 3.828A pdb=" N LEU H 361 " --> pdb=" O GLU H 357 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN H 362 " --> pdb=" O GLU H 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 357 through 362' Processing helix chain 'H' and resid 421 through 427 Processing helix chain 'K' and resid 252 through 258 Processing helix chain 'K' and resid 297 through 301 removed outlier: 4.539A pdb=" N GLY K 300 " --> pdb=" O ASP K 297 " (cutoff:3.500A) Processing helix chain 'K' and resid 312 through 318 Processing helix chain 'K' and resid 356 through 360 Processing helix chain 'K' and resid 421 through 427 Processing helix chain 'L' and resid 356 through 360 removed outlier: 3.713A pdb=" N ALA L 360 " --> pdb=" O GLU L 357 " (cutoff:3.500A) Processing helix chain 'L' and resid 420 through 426 removed outlier: 3.931A pdb=" N TRP L 424 " --> pdb=" O ALA L 420 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 245 through 248 Processing sheet with id=AA2, first strand: chain 'A' and resid 278 through 281 Processing sheet with id=AA3, first strand: chain 'A' and resid 348 through 352 removed outlier: 3.835A pdb=" N THR A 368 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N TYR A 411 " --> pdb=" O GLY A 373 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 352 removed outlier: 3.835A pdb=" N THR A 368 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N TYR A 411 " --> pdb=" O GLY A 373 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 388 through 389 Processing sheet with id=AA6, first strand: chain 'D' and resid 60 through 63 removed outlier: 6.304A pdb=" N ILE K 458 " --> pdb=" O ASN L 459 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N SER L 461 " --> pdb=" O ILE K 458 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL K 460 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N VAL L 463 " --> pdb=" O VAL K 460 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL K 462 " --> pdb=" O VAL L 463 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 245 through 249 removed outlier: 3.759A pdb=" N SER B 247 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR B 267 " --> pdb=" O SER B 247 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR B 265 " --> pdb=" O HIS B 249 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N THR B 265 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU B 308 " --> pdb=" O THR B 265 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N THR B 267 " --> pdb=" O SER B 306 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N SER B 306 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N THR B 269 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL B 304 " --> pdb=" O THR B 269 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 320 through 325 removed outlier: 3.517A pdb=" N ALA B 325 " --> pdb=" O LEU B 334 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 348 through 352 removed outlier: 3.747A pdb=" N THR B 368 " --> pdb=" O LEU B 352 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N TYR B 411 " --> pdb=" O GLY B 373 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 348 through 352 removed outlier: 3.747A pdb=" N THR B 368 " --> pdb=" O LEU B 352 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N TYR B 411 " --> pdb=" O GLY B 373 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 388 through 389 Processing sheet with id=AB3, first strand: chain 'C' and resid 9 through 13 removed outlier: 6.453A pdb=" N VAL C 10 " --> pdb=" O GLU C 108 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N SER C 110 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N SER C 12 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE C 103 " --> pdb=" O CYS C 92 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY C 93 " --> pdb=" O TYR C 36 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR C 36 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N TRP C 37 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 18 through 23 removed outlier: 3.575A pdb=" N ILE C 79 " --> pdb=" O VAL C 18 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 122 through 125 removed outlier: 6.571A pdb=" N TYR C 122 " --> pdb=" O GLN C 218 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N LEU C 220 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL C 124 " --> pdb=" O LEU C 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AB7, first strand: chain 'C' and resid 147 through 149 removed outlier: 3.559A pdb=" N LEU C 201 " --> pdb=" O TYR C 148 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS C 213 " --> pdb=" O CYS C 202 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 225 through 229 removed outlier: 6.123A pdb=" N GLU C 225 " --> pdb=" O GLN C 325 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N PHE C 327 " --> pdb=" O GLU C 225 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL C 227 " --> pdb=" O PHE C 327 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU C 252 " --> pdb=" O VAL C 264 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 234 through 239 Processing sheet with id=AC1, first strand: chain 'C' and resid 340 through 344 removed outlier: 6.260A pdb=" N VAL C 341 " --> pdb=" O LYS C 438 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ILE C 440 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N GLY C 343 " --> pdb=" O ILE C 440 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR C 433 " --> pdb=" O CYS C 423 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY C 419 " --> pdb=" O ILE C 437 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL C 381 " --> pdb=" O TRP C 366 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 349 through 354 removed outlier: 3.517A pdb=" N LEU C 410 " --> pdb=" O VAL C 349 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL C 408 " --> pdb=" O VAL C 351 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 460 through 461 Processing sheet with id=AC4, first strand: chain 'C' and resid 474 through 479 removed outlier: 3.775A pdb=" N TYR C 476 " --> pdb=" O GLY C 527 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TRP C 525 " --> pdb=" O CYS C 478 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N TYR C 524 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ALA C 539 " --> pdb=" O TYR C 524 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N CYS C 526 " --> pdb=" O THR C 537 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR C 537 " --> pdb=" O CYS C 526 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N VAL C 528 " --> pdb=" O GLY C 535 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE C 533 " --> pdb=" O GLN C 530 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 6 through 11 removed outlier: 5.460A pdb=" N VAL D 7 " --> pdb=" O SER D 20 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N SER D 20 " --> pdb=" O VAL D 7 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ASN E 459 " --> pdb=" O VAL H 460 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N VAL H 462 " --> pdb=" O ASN E 459 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N SER E 461 " --> pdb=" O VAL H 462 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 75 through 77 Processing sheet with id=AC7, first strand: chain 'D' and resid 111 through 114 Processing sheet with id=AC8, first strand: chain 'F' and resid 245 through 249 removed outlier: 3.651A pdb=" N ARG F 245 " --> pdb=" O THR F 269 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR F 269 " --> pdb=" O ARG F 245 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N THR F 265 " --> pdb=" O HIS F 249 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY F 270 " --> pdb=" O TYR F 302 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N TYR F 302 " --> pdb=" O GLY F 270 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 324 through 325 Processing sheet with id=AD1, first strand: chain 'F' and resid 348 through 352 removed outlier: 3.726A pdb=" N THR F 368 " --> pdb=" O LEU F 352 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N TYR F 411 " --> pdb=" O GLY F 373 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 348 through 352 removed outlier: 3.726A pdb=" N THR F 368 " --> pdb=" O LEU F 352 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N TYR F 411 " --> pdb=" O GLY F 373 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 388 through 389 Processing sheet with id=AD4, first strand: chain 'G' and resid 245 through 249 removed outlier: 3.744A pdb=" N ARG G 245 " --> pdb=" O THR G 269 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N HIS G 249 " --> pdb=" O THR G 265 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR G 265 " --> pdb=" O HIS G 249 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU G 264 " --> pdb=" O LEU G 308 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 278 through 281 Processing sheet with id=AD6, first strand: chain 'G' and resid 348 through 352 removed outlier: 3.855A pdb=" N THR G 368 " --> pdb=" O LEU G 352 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N TYR G 411 " --> pdb=" O GLY G 373 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU G 396 " --> pdb=" O ILE G 416 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 348 through 352 removed outlier: 3.855A pdb=" N THR G 368 " --> pdb=" O LEU G 352 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N TYR G 411 " --> pdb=" O GLY G 373 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 388 through 389 Processing sheet with id=AD9, first strand: chain 'E' and resid 245 through 248 removed outlier: 4.240A pdb=" N ARG E 245 " --> pdb=" O THR E 269 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR E 269 " --> pdb=" O ARG E 245 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU E 268 " --> pdb=" O VAL E 304 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N GLY E 270 " --> pdb=" O TYR E 302 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N TYR E 302 " --> pdb=" O GLY E 270 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 290 through 291 removed outlier: 4.622A pdb=" N VAL E 290 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL E 307 " --> pdb=" O VAL E 290 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'E' and resid 348 through 351 removed outlier: 3.706A pdb=" N ARG E 372 " --> pdb=" O GLU E 348 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU E 396 " --> pdb=" O ILE E 416 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 348 through 351 removed outlier: 3.706A pdb=" N ARG E 372 " --> pdb=" O GLU E 348 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR E 410 " --> pdb=" O GLU E 403 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 380 through 382 Processing sheet with id=AE5, first strand: chain 'E' and resid 384 through 385 Processing sheet with id=AE6, first strand: chain 'H' and resid 245 through 246 removed outlier: 3.505A pdb=" N ARG H 245 " --> pdb=" O THR H 269 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR H 269 " --> pdb=" O ARG H 245 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'H' and resid 280 through 281 Processing sheet with id=AE8, first strand: chain 'H' and resid 295 through 296 Processing sheet with id=AE9, first strand: chain 'H' and resid 348 through 352 removed outlier: 3.592A pdb=" N GLU H 348 " --> pdb=" O ARG H 372 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR H 368 " --> pdb=" O LEU H 352 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N TYR H 411 " --> pdb=" O GLY H 373 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 348 through 352 removed outlier: 3.592A pdb=" N GLU H 348 " --> pdb=" O ARG H 372 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR H 368 " --> pdb=" O LEU H 352 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N TYR H 411 " --> pdb=" O GLY H 373 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 388 through 389 Processing sheet with id=AF3, first strand: chain 'K' and resid 246 through 248 removed outlier: 4.076A pdb=" N VAL K 307 " --> pdb=" O VAL K 290 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL K 290 " --> pdb=" O VAL K 307 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 278 through 281 removed outlier: 3.642A pdb=" N THR K 278 " --> pdb=" O ALA K 326 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 348 through 352 removed outlier: 4.043A pdb=" N THR K 368 " --> pdb=" O LEU K 352 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL K 365 " --> pdb=" O VAL K 419 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU K 396 " --> pdb=" O ILE K 416 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 348 through 352 removed outlier: 4.043A pdb=" N THR K 368 " --> pdb=" O LEU K 352 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL K 365 " --> pdb=" O VAL K 419 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N THR K 410 " --> pdb=" O GLU K 403 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 388 through 389 removed outlier: 3.526A pdb=" N SER K 431 " --> pdb=" O LEU K 384 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 348 through 352 removed outlier: 3.951A pdb=" N ARG L 372 " --> pdb=" O GLU L 348 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS L 350 " --> pdb=" O LEU L 370 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU L 370 " --> pdb=" O HIS L 350 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU L 352 " --> pdb=" O THR L 368 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N THR L 368 " --> pdb=" O LEU L 352 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU L 396 " --> pdb=" O ILE L 416 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 388 through 389 removed outlier: 3.637A pdb=" N GLN L 388 " --> pdb=" O GLN L 385 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN L 385 " --> pdb=" O GLN L 388 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG L 382 " --> pdb=" O MET L 433 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 401 through 403 removed outlier: 3.692A pdb=" N ARG L 401 " --> pdb=" O ALA L 412 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA L 412 " --> pdb=" O ARG L 401 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THR L 410 " --> pdb=" O GLU L 403 " (cutoff:3.500A) 577 hydrogen bonds defined for protein. 1452 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: 3.26 Time building geometry restraints manager: 2.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5888 1.34 - 1.46: 4375 1.46 - 1.59: 8280 1.59 - 1.71: 0 1.71 - 1.84: 115 Bond restraints: 18658 Sorted by residual: bond pdb=" C1 NAG C 605 " pdb=" O5 NAG C 605 " ideal model delta sigma weight residual 1.406 1.467 -0.061 2.00e-02 2.50e+03 9.17e+00 bond pdb=" C1 NAG G 501 " pdb=" O5 NAG G 501 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.41e+00 bond pdb=" C THR D 54 " pdb=" N SER D 55 " ideal model delta sigma weight residual 1.327 1.300 0.027 1.05e-02 9.07e+03 6.40e+00 bond pdb=" C1 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.80e+00 bond pdb=" C1 NAG B 501 " pdb=" O5 NAG B 501 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.67e+00 ... (remaining 18653 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.22: 25127 3.22 - 6.45: 389 6.45 - 9.67: 62 9.67 - 12.89: 7 12.89 - 16.11: 1 Bond angle restraints: 25586 Sorted by residual: angle pdb=" N SER D 55 " pdb=" CA SER D 55 " pdb=" C SER D 55 " ideal model delta sigma weight residual 108.13 99.01 9.12 9.00e-01 1.23e+00 1.03e+02 angle pdb=" C ASN C 329 " pdb=" N GLU C 330 " pdb=" CA GLU C 330 " ideal model delta sigma weight residual 121.54 131.39 -9.85 1.91e+00 2.74e-01 2.66e+01 angle pdb=" C GLY A 453 " pdb=" N LYS A 454 " pdb=" CA LYS A 454 " ideal model delta sigma weight residual 120.39 127.45 -7.06 1.39e+00 5.18e-01 2.58e+01 angle pdb=" N VAL C 158 " pdb=" CA VAL C 158 " pdb=" C VAL C 158 " ideal model delta sigma weight residual 113.20 108.46 4.74 9.60e-01 1.09e+00 2.43e+01 angle pdb=" CA SER A 260 " pdb=" C SER A 260 " pdb=" N GLU A 261 " ideal model delta sigma weight residual 116.84 125.20 -8.36 1.71e+00 3.42e-01 2.39e+01 ... (remaining 25581 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.88: 10366 19.88 - 39.75: 811 39.75 - 59.63: 121 59.63 - 79.51: 18 79.51 - 99.39: 18 Dihedral angle restraints: 11334 sinusoidal: 4230 harmonic: 7104 Sorted by residual: dihedral pdb=" CB CYS K 299 " pdb=" SG CYS K 299 " pdb=" SG CYS L 242 " pdb=" CB CYS L 242 " ideal model delta sinusoidal sigma weight residual 93.00 -177.19 -89.81 1 1.00e+01 1.00e-02 9.57e+01 dihedral pdb=" CB CYS H 266 " pdb=" SG CYS H 266 " pdb=" SG CYS H 323 " pdb=" CB CYS H 323 " ideal model delta sinusoidal sigma weight residual 93.00 3.83 89.17 1 1.00e+01 1.00e-02 9.46e+01 dihedral pdb=" CB CYS D 109 " pdb=" SG CYS D 109 " pdb=" SG CYS D 134 " pdb=" CB CYS D 134 " ideal model delta sinusoidal sigma weight residual -86.00 -158.33 72.33 1 1.00e+01 1.00e-02 6.69e+01 ... (remaining 11331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 2647 0.085 - 0.170: 391 0.170 - 0.254: 32 0.254 - 0.339: 5 0.339 - 0.424: 5 Chirality restraints: 3080 Sorted by residual: chirality pdb=" C1 NAG C 605 " pdb=" ND2 ASN C 451 " pdb=" C2 NAG C 605 " pdb=" O5 NAG C 605 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.50e+00 chirality pdb=" C2 NAG J 2 " pdb=" C1 NAG J 2 " pdb=" C3 NAG J 2 " pdb=" N2 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.08 -0.42 2.00e-01 2.50e+01 4.32e+00 chirality pdb=" CB ILE E 448 " pdb=" CA ILE E 448 " pdb=" CG1 ILE E 448 " pdb=" CG2 ILE E 448 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.09e+00 ... (remaining 3077 not shown) Planarity restraints: 3287 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU F 403 " -0.050 5.00e-02 4.00e+02 7.48e-02 8.96e+00 pdb=" N PRO F 404 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO F 404 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO F 404 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 327 " -0.046 5.00e-02 4.00e+02 7.06e-02 7.97e+00 pdb=" N PRO B 328 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO B 328 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 328 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 375 " 0.047 5.00e-02 4.00e+02 7.04e-02 7.93e+00 pdb=" N PRO L 376 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO L 376 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO L 376 " 0.039 5.00e-02 4.00e+02 ... (remaining 3284 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3153 2.77 - 3.30: 14380 3.30 - 3.84: 26867 3.84 - 4.37: 28681 4.37 - 4.90: 54365 Nonbonded interactions: 127446 Sorted by model distance: nonbonded pdb=" OG1 THR H 282 " pdb=" OG1 THR H 322 " model vdw 2.241 3.040 nonbonded pdb=" O THR H 280 " pdb=" OG1 THR H 324 " model vdw 2.270 3.040 nonbonded pdb=" OG1 THR L 320 " pdb=" OD1 ASN L 337 " model vdw 2.281 3.040 nonbonded pdb=" OH TYR C 122 " pdb=" OD1 ASN C 133 " model vdw 2.292 3.040 nonbonded pdb=" N ASP D 52 " pdb=" OD1 ASP D 52 " model vdw 2.318 3.120 ... (remaining 127441 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 242 through 244 or (resid 245 and (name N or name CA or na \ me C or name O or name CB )) or resid 246 through 253 or (resid 254 through 255 \ and (name N or name CA or name C or name O or name CB )) or resid 256 through 25 \ 9 or (resid 260 through 262 and (name N or name CA or name C or name O or name C \ B )) or resid 263 through 270 or (resid 271 through 272 and (name N or name CA o \ r name C or name O or name CB )) or resid 276 through 286 or (resid 287 and (nam \ e N or name CA or name C or name O or name CB )) or resid 288 through 312 or (re \ sid 313 and (name N or name CA or name C or name O or name CB )) or resid 314 th \ rough 318 or (resid 319 and (name N or name CA or name C or name O or name CB )) \ or resid 320 through 340 or (resid 341 and (name N or name CA or name C or name \ O or name CB )) or resid 342 through 345 or (resid 346 and (name N or name CA o \ r name C or name O or name CB )) or resid 347 through 356 or (resid 357 through \ 363 and (name N or name CA or name C or name O or name CB )) or resid 364 throug \ h 376 or (resid 377 and (name N or name CA or name C or name O or name CB )) or \ resid 378 through 387 or (resid 388 and (name N or name CA or name C or name O o \ r name CB )) or resid 389 through 391 or (resid 392 through 394 and (name N or n \ ame CA or name C or name O or name CB )) or resid 395 through 404 or (resid 405 \ through 406 and (name N or name CA or name C or name O or name CB )) or resid 40 \ 7 through 424 or (resid 425 through 426 and (name N or name CA or name C or name \ O or name CB )) or resid 427 or (resid 428 and (name N or name CA or name C or \ name O or name CB )) or resid 429 through 445 or (resid 446 and (name N or name \ CA or name C or name O or name CB )) or resid 447 through 449 or (resid 450 and \ (name N or name CA or name C or name O or name CB )) or resid 456 through 464)) selection = (chain 'B' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB )) or resid 256 through 259 or (resid 260 through 262 \ and (name N or name CA or name C or name O or name CB )) or resid 263 through 27 \ 2 or resid 276 through 295 or (resid 296 through 298 and (name N or name CA or n \ ame C or name O or name CB )) or resid 299 through 312 or (resid 313 and (name N \ or name CA or name C or name O or name CB )) or resid 314 through 340 or (resid \ 341 and (name N or name CA or name C or name O or name CB )) or resid 342 throu \ gh 345 or (resid 346 and (name N or name CA or name C or name O or name CB )) or \ resid 347 through 356 or (resid 357 through 363 and (name N or name CA or name \ C or name O or name CB )) or resid 364 through 376 or (resid 377 and (name N or \ name CA or name C or name O or name CB )) or resid 378 through 387 or (resid 388 \ and (name N or name CA or name C or name O or name CB )) or resid 389 through 3 \ 91 or (resid 392 through 394 and (name N or name CA or name C or name O or name \ CB )) or resid 395 through 404 or (resid 405 through 406 and (name N or name CA \ or name C or name O or name CB )) or resid 407 through 424 or (resid 425 through \ 426 and (name N or name CA or name C or name O or name CB )) or resid 427 or (r \ esid 428 and (name N or name CA or name C or name O or name CB )) or resid 429 t \ hrough 445 or (resid 446 and (name N or name CA or name C or name O or name CB ) \ ) or resid 447 through 449 or (resid 450 and (name N or name CA or name C or nam \ e O or name CB )) or resid 456 through 464)) selection = (chain 'E' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB )) or resid 256 through 272 or resid 276 through 450 o \ r resid 456 through 464)) selection = (chain 'F' and (resid 242 through 259 or (resid 260 through 262 and (name N or n \ ame CA or name C or name O or name CB )) or resid 263 through 272 or resid 276 t \ hrough 310 or (resid 311 through 313 and (name N or name CA or name C or name O \ or name CB )) or resid 314 through 340 or (resid 341 and (name N or name CA or n \ ame C or name O or name CB )) or resid 342 through 345 or (resid 346 and (name N \ or name CA or name C or name O or name CB )) or resid 347 through 356 or (resid \ 357 through 363 and (name N or name CA or name C or name O or name CB )) or res \ id 364 through 376 or (resid 377 and (name N or name CA or name C or name O or n \ ame CB )) or resid 378 through 387 or (resid 388 and (name N or name CA or name \ C or name O or name CB )) or resid 389 through 391 or (resid 392 through 394 and \ (name N or name CA or name C or name O or name CB )) or resid 395 through 404 o \ r (resid 405 through 406 and (name N or name CA or name C or name O or name CB ) \ ) or resid 407 through 424 or (resid 425 through 426 and (name N or name CA or n \ ame C or name O or name CB )) or resid 427 through 445 or (resid 446 and (name N \ or name CA or name C or name O or name CB )) or resid 447 through 449 or (resid \ 450 and (name N or name CA or name C or name O or name CB )) or resid 456 throu \ gh 464)) selection = (chain 'G' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB )) or resid 256 through 259 or (resid 260 through 262 \ and (name N or name CA or name C or name O or name CB )) or resid 263 through 27 \ 2 or resid 276 through 316 or (resid 317 and (name N or name CA or name C or nam \ e O or name CB )) or resid 318 through 340 or (resid 341 and (name N or name CA \ or name C or name O or name CB )) or resid 342 through 345 or (resid 346 and (na \ me N or name CA or name C or name O or name CB )) or resid 347 through 356 or (r \ esid 357 through 363 and (name N or name CA or name C or name O or name CB )) or \ resid 364 through 376 or (resid 377 and (name N or name CA or name C or name O \ or name CB )) or resid 378 through 387 or (resid 388 and (name N or name CA or n \ ame C or name O or name CB )) or resid 389 through 391 or (resid 392 through 394 \ and (name N or name CA or name C or name O or name CB )) or resid 395 through 4 \ 04 or (resid 405 through 406 and (name N or name CA or name C or name O or name \ CB )) or resid 407 through 421 or (resid 422 and (name N or name CA or name C or \ name O or name CB )) or resid 423 through 424 or (resid 425 through 426 and (na \ me N or name CA or name C or name O or name CB )) or resid 427 through 445 or (r \ esid 446 and (name N or name CA or name C or name O or name CB )) or resid 447 t \ hrough 449 or (resid 450 and (name N or name CA or name C or name O or name CB ) \ ) or resid 456 through 464)) selection = (chain 'H' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB )) or resid 256 through 272 or resid 276 through 312 o \ r (resid 313 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 14 through 424 or (resid 425 through 426 and (name N or name CA or name C or nam \ e O or name CB )) or resid 427 through 450 or resid 456 through 464)) selection = (chain 'K' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB )) or resid 256 through 259 or (resid 260 through 262 \ and (name N or name CA or name C or name O or name CB )) or resid 263 through 27 \ 2 or resid 276 through 312 or (resid 313 and (name N or name CA or name C or nam \ e O or name CB )) or resid 314 through 316 or (resid 317 and (name N or name CA \ or name C or name O or name CB )) or resid 318 through 340 or (resid 341 and (na \ me N or name CA or name C or name O or name CB )) or resid 342 through 345 or (r \ esid 346 and (name N or name CA or name C or name O or name CB )) or resid 347 t \ hrough 356 or (resid 357 through 363 and (name N or name CA or name C or name O \ or name CB )) or resid 364 through 376 or (resid 377 and (name N or name CA or n \ ame C or name O or name CB )) or resid 378 through 387 or (resid 388 and (name N \ or name CA or name C or name O or name CB )) or resid 389 through 392 or (resid \ 393 through 394 and (name N or name CA or name C or name O or name CB )) or res \ id 395 through 404 or (resid 405 through 406 and (name N or name CA or name C or \ name O or name CB )) or resid 407 through 445 or (resid 446 and (name N or name \ CA or name C or name O or name CB )) or resid 447 through 450 or resid 456 thro \ ugh 464)) selection = (chain 'L' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB )) or resid 256 through 259 or (resid 260 through 262 \ and (name N or name CA or name C or name O or name CB )) or resid 263 through 27 \ 2 or resid 276 through 345 or (resid 346 and (name N or name CA or name C or nam \ e O or name CB )) or resid 347 through 358 or (resid 359 through 363 and (name N \ or name CA or name C or name O or name CB )) or resid 364 through 376 or (resid \ 377 and (name N or name CA or name C or name O or name CB )) or resid 378 throu \ gh 392 or (resid 393 through 394 and (name N or name CA or name C or name O or n \ ame CB )) or resid 395 through 425 or (resid 426 and (name N or name CA or name \ C or name O or name CB )) or resid 427 through 450 or resid 456 through 464)) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.930 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: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.620 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 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:8.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3798 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 : 0.007 0.072 18707 Z= 0.298 Angle : 1.068 16.113 25696 Z= 0.562 Chirality : 0.062 0.424 3080 Planarity : 0.008 0.075 3278 Dihedral : 14.612 99.386 6625 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.23 % Favored : 88.77 % Rotamer: Outliers : 0.32 % Allowed : 9.85 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 1.16 % Twisted General : 0.09 % 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: -3.87 (0.14), residues: 2439 helix: -4.23 (0.21), residues: 143 sheet: -1.61 (0.16), residues: 863 loop : -3.14 (0.13), residues: 1433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 43 TYR 0.019 0.003 TYR G 395 PHE 0.031 0.003 PHE C 136 TRP 0.016 0.002 TRP L 315 HIS 0.007 0.001 HIS K 243 Details of bonding type rmsd covalent geometry : bond 0.00673 (18658) covalent geometry : angle 1.04921 (25586) SS BOND : bond 0.00659 ( 37) SS BOND : angle 1.77700 ( 74) hydrogen bonds : bond 0.29066 ( 485) hydrogen bonds : angle 8.89482 ( 1452) link_BETA1-4 : bond 0.01737 ( 3) link_BETA1-4 : angle 3.29532 ( 9) link_NAG-ASN : bond 0.01075 ( 9) link_NAG-ASN : angle 5.41490 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 539 time to evaluate : 0.687 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: K 327 HIS cc_start: 0.4382 (p90) cc_final: 0.4129 (p90) REVERT: K 365 VAL cc_start: 0.4065 (m) cc_final: 0.3552 (m) outliers start: 6 outliers final: 3 residues processed: 544 average time/residue: 0.4808 time to fit residues: 299.3203 Evaluate side-chains 262 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 259 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain F residue 423 ASP Chi-restraints excluded: chain G residue 393 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 216 optimal weight: 0.3980 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 0.0570 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.0980 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 6.9990 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN A 291 GLN ** A 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 HIS B 406 GLN C 209 ASN D 11 ASN D 30 ASN D 37 ASN D 90 ASN F 362 ASN F 459 ASN G 263 ASN G 291 GLN G 459 ASN E 327 HIS E 459 ASN H 243 HIS H 249 HIS ** H 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 316 ASN ** H 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 457 HIS H 459 ASN K 243 HIS ** K 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 457 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.123537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.091025 restraints weight = 46391.298| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 4.23 r_work: 0.3340 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5942 moved from start: 0.5431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 18707 Z= 0.267 Angle : 1.112 15.599 25696 Z= 0.526 Chirality : 0.056 0.383 3080 Planarity : 0.008 0.095 3278 Dihedral : 8.383 59.043 2855 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 8.63 % Allowed : 18.85 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % 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: -3.13 (0.15), residues: 2439 helix: -3.22 (0.30), residues: 130 sheet: -1.01 (0.17), residues: 810 loop : -2.73 (0.14), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 250 TYR 0.027 0.003 TYR D 110 PHE 0.035 0.003 PHE H 443 TRP 0.034 0.003 TRP C 431 HIS 0.009 0.002 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00597 (18658) covalent geometry : angle 1.09475 (25586) SS BOND : bond 0.01610 ( 37) SS BOND : angle 1.79593 ( 74) hydrogen bonds : bond 0.05001 ( 485) hydrogen bonds : angle 6.35398 ( 1452) link_BETA1-4 : bond 0.00957 ( 3) link_BETA1-4 : angle 5.01101 ( 9) link_NAG-ASN : bond 0.01661 ( 9) link_NAG-ASN : angle 4.92546 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 404 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 MET cc_start: 0.7765 (tpp) cc_final: 0.7554 (tmm) REVERT: B 348 GLU cc_start: 0.7153 (mm-30) cc_final: 0.6948 (mm-30) REVERT: C 32 HIS cc_start: 0.6298 (OUTLIER) cc_final: 0.5351 (t-90) REVERT: C 310 HIS cc_start: 0.6861 (OUTLIER) cc_final: 0.6578 (m170) REVERT: D 12 LYS cc_start: 0.7356 (OUTLIER) cc_final: 0.7053 (tppp) REVERT: D 110 TYR cc_start: 0.7800 (m-80) cc_final: 0.7477 (m-80) REVERT: D 124 MET cc_start: 0.7088 (OUTLIER) cc_final: 0.6861 (mmp) REVERT: F 269 THR cc_start: 0.6455 (p) cc_final: 0.6156 (t) REVERT: F 433 MET cc_start: 0.3868 (tpt) cc_final: 0.3626 (tpt) REVERT: G 401 ARG cc_start: 0.6104 (OUTLIER) cc_final: 0.5470 (ptp-170) REVERT: E 291 GLN cc_start: 0.6633 (pp30) cc_final: 0.6102 (tm130) REVERT: H 316 ASN cc_start: 0.8971 (OUTLIER) cc_final: 0.8670 (p0) REVERT: H 382 ARG cc_start: 0.8245 (mmt180) cc_final: 0.8012 (mmp80) REVERT: K 253 LEU cc_start: 0.7668 (mm) cc_final: 0.7434 (mm) REVERT: K 307 VAL cc_start: 0.3557 (OUTLIER) cc_final: 0.3182 (t) REVERT: K 357 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8238 (pm20) REVERT: L 393 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7099 (pp20) REVERT: L 411 TYR cc_start: 0.4687 (m-10) cc_final: 0.3929 (m-80) outliers start: 162 outliers final: 57 residues processed: 515 average time/residue: 0.4083 time to fit residues: 246.9510 Evaluate side-chains 369 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 304 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 281 TRP Chi-restraints excluded: chain B residue 345 PHE Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain C residue 32 HIS Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 310 HIS Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain D residue 12 LYS Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 124 MET Chi-restraints excluded: chain F residue 249 HIS Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 462 VAL Chi-restraints excluded: chain G residue 306 SER Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 338 ILE Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 401 ARG Chi-restraints excluded: chain G residue 458 ILE Chi-restraints excluded: chain G residue 460 VAL Chi-restraints excluded: chain G residue 462 VAL Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 368 THR Chi-restraints excluded: chain E residue 374 PHE Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 316 ASN Chi-restraints excluded: chain H residue 424 TRP Chi-restraints excluded: chain H residue 448 ILE Chi-restraints excluded: chain H residue 458 ILE Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain K residue 307 VAL Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 357 GLU Chi-restraints excluded: chain K residue 367 LEU Chi-restraints excluded: chain K residue 396 LEU Chi-restraints excluded: chain K residue 400 SER Chi-restraints excluded: chain K residue 439 LEU Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 456 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 19 optimal weight: 0.0980 chunk 122 optimal weight: 0.9990 chunk 31 optimal weight: 0.0470 chunk 168 optimal weight: 0.0970 chunk 67 optimal weight: 9.9990 chunk 119 optimal weight: 0.7980 chunk 208 optimal weight: 9.9990 chunk 153 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 200 optimal weight: 0.0010 chunk 156 optimal weight: 0.9980 overall best weight: 0.2082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 HIS A 385 GLN A 445 GLN C 78 ASN C 530 GLN D 88 GLN D 107 ASN F 316 ASN ** G 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 243 HIS ** H 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 316 ASN H 445 GLN K 350 HIS K 362 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.124492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.092393 restraints weight = 46656.207| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 4.25 r_work: 0.3380 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6055 moved from start: 0.6102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 18707 Z= 0.142 Angle : 0.872 12.543 25696 Z= 0.405 Chirality : 0.047 0.377 3080 Planarity : 0.006 0.056 3278 Dihedral : 7.057 56.620 2848 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 6.71 % Allowed : 25.19 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.53 (0.16), residues: 2439 helix: -2.45 (0.35), residues: 138 sheet: -0.47 (0.18), residues: 803 loop : -2.43 (0.14), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 298 TYR 0.018 0.001 TYR C 90 PHE 0.028 0.002 PHE E 374 TRP 0.040 0.001 TRP C 37 HIS 0.008 0.001 HIS F 327 Details of bonding type rmsd covalent geometry : bond 0.00329 (18658) covalent geometry : angle 0.86044 (25586) SS BOND : bond 0.00487 ( 37) SS BOND : angle 1.34850 ( 74) hydrogen bonds : bond 0.03771 ( 485) hydrogen bonds : angle 5.53461 ( 1452) link_BETA1-4 : bond 0.00495 ( 3) link_BETA1-4 : angle 2.92651 ( 9) link_NAG-ASN : bond 0.00915 ( 9) link_NAG-ASN : angle 3.83897 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 332 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 MET cc_start: 0.7928 (tpp) cc_final: 0.7657 (tmm) REVERT: C 89 ARG cc_start: 0.6487 (pmm-80) cc_final: 0.6287 (pmm-80) REVERT: D 110 TYR cc_start: 0.7764 (m-80) cc_final: 0.7556 (m-80) REVERT: F 316 ASN cc_start: 0.7106 (t0) cc_final: 0.6125 (p0) REVERT: F 464 MET cc_start: 0.7450 (ttm) cc_final: 0.7022 (tmm) REVERT: G 377 LYS cc_start: 0.5742 (OUTLIER) cc_final: 0.5140 (tmmm) REVERT: G 401 ARG cc_start: 0.5588 (OUTLIER) cc_final: 0.5325 (ptp-170) REVERT: E 378 ASP cc_start: 0.7963 (t0) cc_final: 0.7611 (t0) REVERT: E 402 GLN cc_start: 0.7840 (tp40) cc_final: 0.7592 (tp40) REVERT: H 315 TRP cc_start: 0.6473 (t-100) cc_final: 0.5906 (t60) REVERT: H 415 SER cc_start: 0.7639 (m) cc_final: 0.7406 (p) REVERT: K 291 GLN cc_start: 0.6642 (OUTLIER) cc_final: 0.6073 (mp-120) REVERT: K 449 ASP cc_start: 0.4413 (t70) cc_final: 0.4165 (t0) REVERT: L 378 ASP cc_start: 0.6477 (t0) cc_final: 0.6033 (t0) REVERT: L 393 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7198 (pp20) REVERT: L 411 TYR cc_start: 0.4721 (m-10) cc_final: 0.3906 (m-80) outliers start: 126 outliers final: 48 residues processed: 413 average time/residue: 0.4160 time to fit residues: 204.0175 Evaluate side-chains 336 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 285 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 281 TRP Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 16 ASN Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain F residue 249 HIS Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 458 ILE Chi-restraints excluded: chain F residue 460 VAL Chi-restraints excluded: chain F residue 462 VAL Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 304 VAL Chi-restraints excluded: chain G residue 306 SER Chi-restraints excluded: chain G residue 364 LEU Chi-restraints excluded: chain G residue 368 THR Chi-restraints excluded: chain G residue 377 LYS Chi-restraints excluded: chain G residue 401 ARG Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 460 VAL Chi-restraints excluded: chain G residue 462 VAL Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain H residue 316 ASN Chi-restraints excluded: chain H residue 323 CYS Chi-restraints excluded: chain H residue 368 THR Chi-restraints excluded: chain H residue 458 ILE Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain K residue 291 GLN Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 365 VAL Chi-restraints excluded: chain K residue 396 LEU Chi-restraints excluded: chain K residue 439 LEU Chi-restraints excluded: chain L residue 365 VAL 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: 50.3904 > 50: distance: 27 - 32: 20.840 distance: 32 - 33: 30.053 distance: 33 - 34: 22.116 distance: 33 - 36: 5.918 distance: 34 - 35: 22.738 distance: 34 - 39: 10.534 distance: 36 - 37: 24.954 distance: 36 - 38: 20.813 distance: 39 - 40: 20.656 distance: 39 - 187: 13.662 distance: 40 - 41: 8.970 distance: 40 - 43: 10.497 distance: 41 - 42: 33.082 distance: 41 - 50: 17.235 distance: 42 - 184: 28.145 distance: 43 - 44: 10.366 distance: 44 - 45: 11.906 distance: 46 - 47: 3.639 distance: 50 - 51: 12.053 distance: 51 - 52: 19.780 distance: 51 - 54: 15.911 distance: 52 - 53: 22.880 distance: 52 - 64: 20.240 distance: 54 - 55: 31.666 distance: 55 - 56: 16.964 distance: 55 - 57: 14.947 distance: 56 - 58: 7.066 distance: 57 - 59: 8.028 distance: 59 - 61: 5.457 distance: 60 - 62: 6.195 distance: 61 - 63: 5.001 distance: 62 - 63: 7.737 distance: 64 - 65: 18.459 distance: 65 - 66: 9.921 distance: 65 - 68: 17.983 distance: 66 - 67: 22.203 distance: 66 - 72: 7.933 distance: 68 - 69: 9.649 distance: 69 - 70: 14.572 distance: 69 - 71: 10.218 distance: 72 - 73: 14.910 distance: 72 - 94: 21.479 distance: 73 - 74: 16.474 distance: 73 - 76: 7.685 distance: 74 - 75: 29.789 distance: 74 - 81: 19.458 distance: 75 - 91: 41.801 distance: 76 - 77: 16.476 distance: 77 - 78: 8.601 distance: 78 - 79: 6.855 distance: 78 - 80: 4.996 distance: 81 - 82: 22.779 distance: 82 - 83: 33.818 distance: 83 - 84: 21.451 distance: 83 - 85: 15.742 distance: 85 - 86: 9.965 distance: 86 - 87: 18.516 distance: 86 - 89: 22.154 distance: 87 - 88: 36.581 distance: 87 - 91: 27.519 distance: 89 - 90: 8.104 distance: 91 - 92: 7.186 distance: 92 - 93: 34.440 distance: 92 - 95: 33.956 distance: 93 - 94: 16.720 distance: 93 - 100: 18.150 distance: 95 - 96: 31.832 distance: 96 - 97: 13.738 distance: 97 - 98: 11.772 distance: 97 - 99: 3.272 distance: 100 - 101: 40.637 distance: 101 - 102: 25.589 distance: 101 - 104: 29.212 distance: 102 - 103: 23.170 distance: 102 - 109: 11.756 distance: 104 - 105: 18.755 distance: 105 - 106: 18.456 distance: 106 - 107: 15.832 distance: 106 - 108: 11.207 distance: 109 - 110: 30.216 distance: 110 - 111: 19.573 distance: 110 - 113: 16.245 distance: 111 - 112: 39.870 distance: 111 - 117: 21.367 distance: 113 - 114: 22.482 distance: 114 - 115: 20.949 distance: 114 - 116: 26.736 distance: 139 - 149: 3.005