Starting phenix.real_space_refine on Mon May 19 11:01:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ue8_20750/05_2025/6ue8_20750.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ue8_20750/05_2025/6ue8_20750.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ue8_20750/05_2025/6ue8_20750.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ue8_20750/05_2025/6ue8_20750.map" model { file = "/net/cci-nas-00/data/ceres_data/6ue8_20750/05_2025/6ue8_20750.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ue8_20750/05_2025/6ue8_20750.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= -0.012 sd= 0.434 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 11463 2.51 5 N 3144 2.21 5 O 3478 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 18183 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: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} 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: {'TYR:plan': 1, 'GLU:plan': 6, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "C" Number of atoms: 4130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4130 Classifications: {'peptide': 535} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 509} 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: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1042 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 123} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 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: {'GLN:plan1': 1, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 3} 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: {'TYR:plan': 1, 'GLU:plan': 8, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 2} 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: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 11, 'ARG:plan': 6} 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: {'GLN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 11, 'ARG:plan': 6} 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: {'TYR:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5, 'GLN:plan1': 1, 'ASP:plan': 2} 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: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 5} 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: 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: "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: 12.24, per 1000 atoms: 0.67 Number of scatterers: 18183 At special positions: 0 Unit cell: (173.196, 147.726, 180.328, 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 3478 8.00 N 3144 7.00 C 11463 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A 369 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 323 " distance=2.03 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C 253 " - pdb=" SG CYS C 261 " distance=2.03 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 377 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS D 13 " - pdb=" SG CYS D 101 " distance=2.03 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS F 471 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS F 242 " - pdb=" SG CYS G 299 " distance=2.03 Simple disulfide: pdb=" SG CYS F 266 " - pdb=" SG CYS F 323 " distance=2.03 Simple disulfide: pdb=" SG CYS F 299 " - pdb=" SG CYS G 242 " distance=2.04 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=2.03 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=2.02 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=2.03 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=2.03 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=2.03 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 603 " - " ASN C 65 " " 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: 4.28 Conformation dependent library (CDL) restraints added in 2.4 seconds 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4594 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 53 sheets defined 10.0% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.64 Creating SS restraints... Processing helix chain 'A' and resid 252 through 258 removed outlier: 3.606A pdb=" N LEU A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 317 removed outlier: 3.672A pdb=" N ASN A 316 " --> pdb=" O ALA A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 395 removed outlier: 3.537A pdb=" N LYS A 394 " --> pdb=" O PRO A 391 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR A 395 " --> pdb=" O ARG A 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 391 through 395' Processing helix chain 'A' and resid 421 through 427 removed outlier: 3.953A pdb=" N GLY A 427 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 258 Processing helix chain 'B' and resid 312 through 318 Processing helix chain 'B' and resid 357 through 362 removed outlier: 4.205A pdb=" N LEU B 361 " --> pdb=" O GLU B 357 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN B 362 " --> pdb=" O GLU B 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 357 through 362' 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 422 through 427 Processing helix chain 'C' and resid 27 through 33 removed outlier: 3.681A pdb=" N HIS C 32 " --> pdb=" O SER C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 246 Processing helix chain 'C' and resid 272 through 276 removed outlier: 3.849A pdb=" N PHE C 275 " --> pdb=" O ALA C 272 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU C 276 " --> pdb=" O PRO C 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 272 through 276' Processing helix chain 'C' and resid 298 through 302 removed outlier: 3.596A pdb=" N ASP C 301 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 4.054A 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: 3.690A pdb=" N SER C 360 " --> pdb=" O ARG C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 472 removed outlier: 3.717A pdb=" N SER C 471 " --> pdb=" O CYS C 468 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER C 472 " --> pdb=" O LYS C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 517 through 521 removed outlier: 4.292A pdb=" N ASP C 520 " --> pdb=" O THR C 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 69 Processing helix chain 'F' and resid 253 through 258 Processing helix chain 'F' and resid 312 through 318 removed outlier: 4.175A pdb=" N ASN F 316 " --> pdb=" O ALA F 312 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS F 317 " --> pdb=" O GLN F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 360 removed outlier: 3.730A pdb=" N LEU F 359 " --> pdb=" O PRO F 355 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA F 360 " --> pdb=" O SER F 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 355 through 360' 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: 3.895A pdb=" N LYS F 425 " --> pdb=" O ALA F 421 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 257 Processing helix chain 'G' and resid 355 through 360 removed outlier: 3.679A pdb=" N LEU G 359 " --> pdb=" O PRO G 355 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA G 360 " --> pdb=" O SER G 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 355 through 360' Processing helix chain 'G' and resid 421 through 427 removed outlier: 3.709A pdb=" N GLY G 427 " --> pdb=" O ASP G 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 316 removed outlier: 3.628A pdb=" N TRP E 315 " --> pdb=" O ALA E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 362 removed outlier: 4.439A pdb=" N LEU E 361 " --> pdb=" O GLU E 357 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN E 362 " --> pdb=" O GLU E 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 357 through 362' Processing helix chain 'E' and resid 391 through 395 removed outlier: 4.264A pdb=" N TYR E 395 " --> pdb=" O ARG E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 427 Processing helix chain 'H' and resid 252 through 258 removed outlier: 3.850A pdb=" N LEU H 258 " --> pdb=" O GLU H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 298 through 300 No H-bonds generated for 'chain 'H' and resid 298 through 300' Processing helix chain 'H' and resid 311 through 316 removed outlier: 3.522A pdb=" N TRP H 315 " --> pdb=" O CYS H 311 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN H 316 " --> pdb=" O ALA H 312 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 311 through 316' Processing helix chain 'H' and resid 357 through 362 removed outlier: 3.716A pdb=" N LEU H 361 " --> pdb=" O GLU H 357 " (cutoff:3.500A) removed outlier: 3.745A 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 391 through 395 removed outlier: 4.133A pdb=" N TYR H 395 " --> pdb=" O ARG H 392 " (cutoff:3.500A) Processing helix chain 'H' and resid 421 through 427 Processing helix chain 'K' and resid 252 through 258 Processing helix chain 'K' and resid 312 through 318 removed outlier: 3.610A pdb=" N GLY K 318 " --> pdb=" O PRO K 314 " (cutoff:3.500A) Processing helix chain 'K' and resid 356 through 362 removed outlier: 3.652A pdb=" N LEU K 361 " --> pdb=" O GLU K 357 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN K 362 " --> pdb=" O GLU K 358 " (cutoff:3.500A) Processing helix chain 'K' and resid 420 through 427 removed outlier: 3.905A pdb=" N TRP K 424 " --> pdb=" O ALA K 420 " (cutoff:3.500A) Processing helix chain 'L' and resid 252 through 256 removed outlier: 3.869A pdb=" N ASP L 255 " --> pdb=" O ALA L 252 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU L 256 " --> pdb=" O LEU L 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 252 through 256' Processing helix chain 'L' and resid 356 through 360 removed outlier: 3.884A pdb=" N ALA L 360 " --> pdb=" O GLU L 357 " (cutoff:3.500A) Processing helix chain 'L' and resid 421 through 426 Processing sheet with id=AA1, first strand: chain 'A' and resid 246 through 247 removed outlier: 3.620A pdb=" N SER A 247 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR A 267 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 290 " --> pdb=" O VAL A 307 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 280 through 281 removed outlier: 3.540A pdb=" N ALA A 336 " --> pdb=" O CYS A 323 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 348 through 352 removed outlier: 3.907A pdb=" N THR A 368 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 5.845A 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: 3.907A pdb=" N THR A 368 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N TYR A 411 " --> pdb=" O GLY A 373 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N THR A 410 " --> pdb=" O GLU A 403 " (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: 8.198A pdb=" N PHE D 61 " --> pdb=" O ASN B 459 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N SER B 461 " --> pdb=" O PHE D 61 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N TYR D 63 " --> pdb=" O SER B 461 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL B 463 " --> pdb=" O TYR D 63 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE K 458 " --> pdb=" O HIS L 457 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL K 460 " --> pdb=" O ASN L 459 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 245 through 249 removed outlier: 3.754A pdb=" N ARG B 245 " --> pdb=" O THR B 269 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR B 265 " --> pdb=" O HIS B 249 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY B 270 " --> pdb=" O TYR B 302 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR B 302 " --> pdb=" O GLY B 270 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 280 through 281 removed outlier: 3.595A pdb=" N PHE B 321 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 338 " --> pdb=" O PHE B 321 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 348 through 352 removed outlier: 3.812A pdb=" N THR B 368 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 348 through 352 removed outlier: 3.812A pdb=" N THR B 368 " --> pdb=" O LEU B 352 " (cutoff:3.500A) removed outlier: 5.757A 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: 6.269A pdb=" N VAL C 10 " --> pdb=" O GLU C 108 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N SER C 110 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N SER C 12 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE C 103 " --> pdb=" O CYS C 92 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY C 93 " --> pdb=" O TYR C 36 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR C 36 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N TRP C 37 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 19 through 23 removed outlier: 3.749A pdb=" N ASN C 65 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 123 through 125 removed outlier: 7.068A 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 removed outlier: 3.569A pdb=" N VAL C 130 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE C 189 " --> pdb=" O VAL C 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 149 through 151 removed outlier: 3.580A pdb=" N LYS C 149 " --> pdb=" O VAL C 156 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE C 151 " --> pdb=" O TYR C 154 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR C 154 " --> pdb=" O ILE C 151 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 225 through 229 removed outlier: 3.565A pdb=" N GLU C 225 " --> pdb=" O ALA C 323 " (cutoff:3.500A) removed outlier: 7.270A 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 removed outlier: 3.642A pdb=" N VAL C 292 " --> pdb=" O PHE C 237 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 340 through 343 removed outlier: 3.527A pdb=" N GLY C 343 " --> pdb=" O LYS C 438 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR C 433 " --> pdb=" O CYS C 423 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY C 419 " --> pdb=" O ILE C 437 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 424 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL C 381 " --> pdb=" O TRP C 366 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 348 through 354 removed outlier: 3.607A pdb=" N LEU C 410 " --> pdb=" O VAL C 349 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL C 351 " --> pdb=" O VAL C 408 " (cutoff:3.500A) removed outlier: 3.856A 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 462 removed outlier: 4.015A pdb=" N LEU C 460 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU C 513 " --> pdb=" O LEU C 460 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 511 " --> pdb=" O VAL C 462 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 484 through 487 removed outlier: 3.950A pdb=" N GLN C 486 " --> pdb=" O LYS C 479 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS C 479 " --> pdb=" O GLN C 486 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS C 478 " --> pdb=" O TRP C 525 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N TRP C 523 " --> pdb=" O TRP C 480 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N TYR C 524 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ALA C 539 " --> pdb=" O TYR C 524 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N CYS C 526 " --> pdb=" O THR C 537 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR C 537 " --> pdb=" O CYS C 526 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N VAL C 528 " --> pdb=" O GLY C 535 " (cutoff:3.500A) removed outlier: 4.026A 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: 6.772A pdb=" N ILE D 18 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ASP D 10 " --> pdb=" O ALA D 16 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA D 16 " --> pdb=" O ASP D 10 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE D 33 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL D 34 " --> pdb=" O HIS F 457 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ASN F 459 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ARG D 36 " --> pdb=" O ASN F 459 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N SER F 461 " --> pdb=" O ARG D 36 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE D 38 " --> pdb=" O SER F 461 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL F 463 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE D 40 " --> pdb=" O VAL F 463 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ALA F 465 " --> pdb=" O ILE D 40 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL D 42 " --> pdb=" O ALA F 465 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE G 458 " --> pdb=" O ASN H 459 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N SER H 461 " --> pdb=" O ILE G 458 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL G 460 " --> pdb=" O SER H 461 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N VAL H 463 " --> pdb=" O VAL G 460 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL G 462 " --> pdb=" O VAL H 463 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 75 through 78 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 247 removed outlier: 3.526A pdb=" N CYS F 266 " --> pdb=" O SER F 306 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU F 268 " --> pdb=" O VAL F 304 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL F 304 " --> pdb=" O LEU F 268 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY F 270 " --> pdb=" O TYR F 302 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N TYR F 302 " --> pdb=" O GLY F 270 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 279 through 280 removed outlier: 3.661A pdb=" N ALA F 325 " --> pdb=" O LEU F 334 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU F 334 " --> pdb=" O ALA F 325 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 348 through 352 removed outlier: 3.804A pdb=" N THR F 368 " --> pdb=" O LEU F 352 " (cutoff:3.500A) removed outlier: 5.575A 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: 3.804A pdb=" N THR F 368 " --> pdb=" O LEU F 352 " (cutoff:3.500A) removed outlier: 5.575A 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 322 through 323 Processing sheet with id=AD5, first strand: chain 'G' and resid 348 through 352 removed outlier: 4.016A pdb=" N THR G 368 " --> pdb=" O LEU G 352 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N TYR G 411 " --> pdb=" O GLY G 373 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU G 396 " --> pdb=" O ILE G 416 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 348 through 352 removed outlier: 4.016A pdb=" N THR G 368 " --> pdb=" O LEU G 352 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N TYR G 411 " --> pdb=" O GLY G 373 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 388 through 389 Processing sheet with id=AD8, first strand: chain 'E' and resid 245 through 249 Processing sheet with id=AD9, first strand: chain 'E' and resid 295 through 297 removed outlier: 3.678A pdb=" N SER E 303 " --> pdb=" O GLU E 295 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP E 297 " --> pdb=" O CYS E 301 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N CYS E 301 " --> pdb=" O ASP E 297 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 350 through 352 removed outlier: 4.381A pdb=" N THR E 368 " --> pdb=" O LEU E 352 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 350 through 352 removed outlier: 4.381A pdb=" N THR E 368 " --> pdb=" O LEU E 352 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N THR E 410 " --> pdb=" O GLU E 403 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA E 412 " --> pdb=" O ARG E 401 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG E 401 " --> pdb=" O ALA E 412 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 388 through 389 removed outlier: 3.737A pdb=" N GLN E 388 " --> pdb=" O GLN E 385 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN E 385 " --> pdb=" O GLN E 388 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU E 380 " --> pdb=" O GLY E 435 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU E 384 " --> pdb=" O SER E 431 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 245 through 249 removed outlier: 3.522A pdb=" N THR H 269 " --> pdb=" O ARG H 245 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER H 247 " --> pdb=" O THR H 267 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR H 267 " --> pdb=" O SER H 247 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N HIS H 249 " --> pdb=" O THR H 265 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N THR H 265 " --> pdb=" O HIS H 249 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 320 through 322 removed outlier: 3.516A pdb=" N PHE H 321 " --> pdb=" O ILE H 338 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 348 through 352 removed outlier: 4.135A pdb=" N THR H 368 " --> pdb=" O LEU H 352 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N TYR H 411 " --> pdb=" O GLY H 373 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 348 through 352 removed outlier: 4.135A pdb=" N THR H 368 " --> pdb=" O LEU H 352 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N TYR H 411 " --> pdb=" O GLY H 373 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N THR H 410 " --> pdb=" O GLU H 403 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 388 through 389 removed outlier: 3.685A pdb=" N PHE H 430 " --> pdb=" O ILE H 448 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 247 through 248 removed outlier: 4.487A pdb=" N SER K 247 " --> pdb=" O THR K 267 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR K 267 " --> pdb=" O SER K 247 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU K 268 " --> pdb=" O VAL K 304 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL K 304 " --> pdb=" O LEU K 268 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL K 307 " --> pdb=" O VAL K 290 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 247 through 248 removed outlier: 4.487A pdb=" N SER K 247 " --> pdb=" O THR K 267 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR K 267 " --> pdb=" O SER K 247 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU K 268 " --> pdb=" O VAL K 304 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL K 304 " --> pdb=" O LEU K 268 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 278 through 281 removed outlier: 3.501A pdb=" N LEU K 334 " --> pdb=" O ALA K 325 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 348 through 352 removed outlier: 4.058A pdb=" N THR K 368 " --> pdb=" O LEU K 352 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU K 396 " --> pdb=" O ILE K 416 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 348 through 352 removed outlier: 4.058A pdb=" N THR K 368 " --> pdb=" O LEU K 352 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 388 through 389 removed outlier: 3.958A pdb=" N PHE K 430 " --> pdb=" O ILE K 448 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE K 448 " --> pdb=" O PHE K 430 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 350 through 351 removed outlier: 3.723A pdb=" N HIS L 350 " --> pdb=" O LEU L 370 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU L 396 " --> pdb=" O ILE L 416 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 350 through 351 removed outlier: 3.723A pdb=" N HIS L 350 " --> pdb=" O LEU L 370 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 388 through 389 removed outlier: 4.111A pdb=" N GLN L 388 " --> pdb=" O GLN L 385 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN L 385 " --> pdb=" O GLN L 388 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU L 380 " --> pdb=" O GLY L 435 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY L 435 " --> pdb=" O LEU L 380 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG L 382 " --> pdb=" O MET L 433 " (cutoff:3.500A) 546 hydrogen bonds defined for protein. 1398 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: 6.62 Time building geometry restraints manager: 5.09 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: 5827 1.34 - 1.46: 4438 1.46 - 1.59: 8234 1.59 - 1.72: 0 1.72 - 1.84: 115 Bond restraints: 18614 Sorted by residual: bond pdb=" C GLU K 389 " pdb=" N LEU K 390 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.47e-02 4.63e+03 8.79e+00 bond pdb=" C GLU A 389 " pdb=" N LEU A 390 " ideal model delta sigma weight residual 1.331 1.255 0.076 2.83e-02 1.25e+03 7.21e+00 bond pdb=" C1 NAG G 501 " pdb=" O5 NAG G 501 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.69e+00 bond pdb=" N LEU G 359 " pdb=" CA LEU G 359 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.23e-02 6.61e+03 6.11e+00 bond pdb=" N GLU D 35 " pdb=" CA GLU D 35 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.22e-02 6.72e+03 5.89e+00 ... (remaining 18609 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 24400 2.42 - 4.83: 951 4.83 - 7.25: 136 7.25 - 9.67: 31 9.67 - 12.08: 9 Bond angle restraints: 25527 Sorted by residual: angle pdb=" C ALA L 438 " pdb=" N LEU L 439 " pdb=" CA LEU L 439 " ideal model delta sigma weight residual 120.68 131.71 -11.03 1.52e+00 4.33e-01 5.27e+01 angle pdb=" C HIS E 249 " pdb=" N ARG E 250 " pdb=" CA ARG E 250 " ideal model delta sigma weight residual 121.03 131.25 -10.22 1.60e+00 3.91e-01 4.08e+01 angle pdb=" C VAL E 307 " pdb=" N LEU E 308 " pdb=" CA LEU E 308 " ideal model delta sigma weight residual 122.65 132.54 -9.89 1.66e+00 3.63e-01 3.55e+01 angle pdb=" N GLY C 527 " pdb=" CA GLY C 527 " pdb=" C GLY C 527 " ideal model delta sigma weight residual 111.42 119.49 -8.07 1.42e+00 4.96e-01 3.23e+01 angle pdb=" C TRP L 281 " pdb=" N THR L 282 " pdb=" CA THR L 282 " ideal model delta sigma weight residual 120.26 127.47 -7.21 1.34e+00 5.57e-01 2.89e+01 ... (remaining 25522 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.23: 10553 22.23 - 44.46: 646 44.46 - 66.69: 56 66.69 - 88.93: 13 88.93 - 111.16: 13 Dihedral angle restraints: 11281 sinusoidal: 4183 harmonic: 7098 Sorted by residual: 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 93.00 164.04 -71.04 1 1.00e+01 1.00e-02 6.48e+01 dihedral pdb=" CB CYS A 242 " pdb=" SG CYS A 242 " pdb=" SG CYS B 299 " pdb=" CB CYS B 299 " ideal model delta sinusoidal sigma weight residual 93.00 159.61 -66.61 1 1.00e+01 1.00e-02 5.79e+01 dihedral pdb=" CB CYS C 253 " pdb=" SG CYS C 253 " pdb=" SG CYS C 261 " pdb=" CB CYS C 261 " ideal model delta sinusoidal sigma weight residual -86.00 -149.92 63.92 1 1.00e+01 1.00e-02 5.38e+01 ... (remaining 11278 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 2532 0.080 - 0.160: 479 0.160 - 0.239: 49 0.239 - 0.319: 5 0.319 - 0.399: 3 Chirality restraints: 3068 Sorted by residual: 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 -2.09 -0.40 2.00e-01 2.50e+01 3.98e+00 chirality pdb=" CG LEU L 264 " pdb=" CB LEU L 264 " pdb=" CD1 LEU L 264 " pdb=" CD2 LEU L 264 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" C2 NAG A 501 " pdb=" C1 NAG A 501 " pdb=" C3 NAG A 501 " pdb=" N2 NAG A 501 " both_signs ideal model delta sigma weight residual False -2.49 -2.15 -0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 3065 not shown) Planarity restraints: 3280 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 55 " 0.057 5.00e-02 4.00e+02 8.47e-02 1.15e+01 pdb=" N PRO D 56 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO D 56 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 56 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS G 327 " -0.046 5.00e-02 4.00e+02 6.95e-02 7.74e+00 pdb=" N PRO G 328 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO G 328 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO G 328 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR G 282 " 0.045 5.00e-02 4.00e+02 6.68e-02 7.14e+00 pdb=" N PRO G 283 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO G 283 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO G 283 " 0.037 5.00e-02 4.00e+02 ... (remaining 3277 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 707 2.70 - 3.25: 14778 3.25 - 3.80: 25886 3.80 - 4.35: 30411 4.35 - 4.90: 54662 Nonbonded interactions: 126444 Sorted by model distance: nonbonded pdb=" NH2 ARG D 21 " pdb=" OE1 GLU D 35 " model vdw 2.144 3.120 nonbonded pdb=" O LEU C 460 " pdb=" OG1 THR C 512 " model vdw 2.248 3.040 nonbonded pdb=" O SER C 506 " pdb=" OG SER C 506 " model vdw 2.257 3.040 nonbonded pdb=" OG1 THR H 282 " pdb=" OG1 THR H 322 " model vdw 2.275 3.040 nonbonded pdb=" O LEU L 396 " pdb=" OG SER L 415 " model vdw 2.277 3.040 ... (remaining 126439 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.260 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: 0.970 Check model and map are aligned: 0.190 Set scattering table: 0.160 Process input model: 43.620 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 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 : 0.008 0.083 18661 Z= 0.369 Angle : 1.159 12.575 25631 Z= 0.626 Chirality : 0.062 0.399 3068 Planarity : 0.009 0.085 3273 Dihedral : 14.435 111.156 6576 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.65 % Favored : 88.35 % Rotamer: Outliers : 0.48 % Allowed : 9.91 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 1.16 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.88 (0.14), residues: 2437 helix: -4.46 (0.19), residues: 136 sheet: -1.55 (0.17), residues: 783 loop : -3.14 (0.13), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 383 HIS 0.009 0.002 HIS E 436 PHE 0.024 0.003 PHE C 136 TYR 0.024 0.003 TYR A 395 ARG 0.011 0.001 ARG L 250 Details of bonding type rmsd link_NAG-ASN : bond 0.00809 ( 7) link_NAG-ASN : angle 4.91219 ( 21) link_BETA1-4 : bond 0.01107 ( 3) link_BETA1-4 : angle 5.53441 ( 9) hydrogen bonds : bond 0.28877 ( 450) hydrogen bonds : angle 8.92201 ( 1398) SS BOND : bond 0.00591 ( 37) SS BOND : angle 2.11049 ( 74) covalent geometry : bond 0.00835 (18614) covalent geometry : angle 1.14268 (25527) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 450 time to evaluate : 1.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 468 ASP cc_start: 0.8127 (p0) cc_final: 0.7844 (p0) REVERT: K 378 ASP cc_start: 0.7088 (m-30) cc_final: 0.6853 (m-30) REVERT: L 411 TYR cc_start: 0.4961 (m-80) cc_final: 0.4398 (m-80) outliers start: 9 outliers final: 1 residues processed: 457 average time/residue: 1.3142 time to fit residues: 668.9037 Evaluate side-chains 242 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 241 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 434 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 206 optimal weight: 10.0000 chunk 185 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 125 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 192 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 116 optimal weight: 0.5980 chunk 142 optimal weight: 0.6980 chunk 222 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 457 HIS B 343 ASN C 68 ASN C 247 ASN D 81 ASN G 263 ASN ** G 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 459 ASN E 459 ASN ** H 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 459 ASN K 385 GLN L 249 HIS L 459 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.138538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.101395 restraints weight = 45744.297| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 4.40 r_work: 0.3462 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18661 Z= 0.157 Angle : 0.820 11.994 25631 Z= 0.405 Chirality : 0.045 0.247 3068 Planarity : 0.007 0.071 3273 Dihedral : 8.817 71.503 2804 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 4.64 % Allowed : 18.59 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 1.16 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.15), residues: 2437 helix: -3.61 (0.27), residues: 128 sheet: -0.81 (0.18), residues: 809 loop : -2.65 (0.14), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 281 HIS 0.006 0.001 HIS F 457 PHE 0.017 0.001 PHE L 443 TYR 0.014 0.001 TYR C 148 ARG 0.011 0.001 ARG C 336 Details of bonding type rmsd link_NAG-ASN : bond 0.00518 ( 7) link_NAG-ASN : angle 3.07832 ( 21) link_BETA1-4 : bond 0.00606 ( 3) link_BETA1-4 : angle 3.92517 ( 9) hydrogen bonds : bond 0.04191 ( 450) hydrogen bonds : angle 5.78163 ( 1398) SS BOND : bond 0.00433 ( 37) SS BOND : angle 1.71047 ( 74) covalent geometry : bond 0.00348 (18614) covalent geometry : angle 0.80830 (25527) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 288 time to evaluate : 2.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 GLU cc_start: 0.8904 (tt0) cc_final: 0.8660 (tm-30) REVERT: A 390 LEU cc_start: 0.9522 (mp) cc_final: 0.9247 (mm) REVERT: A 403 GLU cc_start: 0.9098 (pt0) cc_final: 0.8739 (pt0) REVERT: A 437 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8487 (mt-10) REVERT: B 385 GLN cc_start: 0.9023 (tp40) cc_final: 0.8723 (tp40) REVERT: B 392 ARG cc_start: 0.9299 (mmm-85) cc_final: 0.8998 (ttp-110) REVERT: B 423 ASP cc_start: 0.8894 (m-30) cc_final: 0.8607 (m-30) REVERT: B 428 GLU cc_start: 0.8186 (mp0) cc_final: 0.7582 (mp0) REVERT: B 464 MET cc_start: 0.7294 (ppp) cc_final: 0.6843 (ppp) REVERT: C 43 ARG cc_start: 0.6892 (mmp80) cc_final: 0.6647 (mmp-170) REVERT: C 111 GLN cc_start: 0.7806 (pp30) cc_final: 0.7596 (pp30) REVERT: C 483 THR cc_start: 0.7467 (OUTLIER) cc_final: 0.7069 (t) REVERT: D 82 GLN cc_start: 0.9118 (mm-40) cc_final: 0.8884 (mp10) REVERT: F 340 LYS cc_start: 0.7953 (ttmt) cc_final: 0.7673 (ttmt) REVERT: E 414 THR cc_start: 0.8482 (OUTLIER) cc_final: 0.8228 (p) REVERT: E 430 PHE cc_start: 0.7121 (m-80) cc_final: 0.6889 (m-80) REVERT: E 448 ILE cc_start: 0.6510 (OUTLIER) cc_final: 0.6036 (pp) REVERT: H 403 GLU cc_start: 0.8000 (pt0) cc_final: 0.6992 (pm20) REVERT: H 433 MET cc_start: 0.8400 (tpp) cc_final: 0.7318 (mmm) REVERT: K 378 ASP cc_start: 0.7445 (m-30) cc_final: 0.7222 (m-30) REVERT: K 418 ARG cc_start: 0.6110 (mtt180) cc_final: 0.5858 (mmt180) REVERT: K 433 MET cc_start: 0.8764 (mmm) cc_final: 0.8538 (mmm) REVERT: L 372 ARG cc_start: 0.6970 (ptm-80) cc_final: 0.6735 (ptm-80) REVERT: L 385 GLN cc_start: 0.6024 (OUTLIER) cc_final: 0.5824 (tp40) REVERT: L 403 GLU cc_start: 0.8827 (pt0) cc_final: 0.8519 (pm20) outliers start: 87 outliers final: 30 residues processed: 345 average time/residue: 1.1668 time to fit residues: 453.8433 Evaluate side-chains 261 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 226 time to evaluate : 1.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain C residue 122 TYR Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 402 GLN Chi-restraints excluded: chain G residue 249 HIS Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 343 ASN Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain E residue 414 THR Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 344 THR Chi-restraints excluded: chain K residue 282 THR Chi-restraints excluded: chain K residue 290 VAL Chi-restraints excluded: chain K residue 396 LEU Chi-restraints excluded: chain K residue 415 SER Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain L residue 278 THR Chi-restraints excluded: chain L residue 335 THR Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 385 GLN Chi-restraints excluded: chain L residue 462 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 174 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 28 optimal weight: 9.9990 chunk 235 optimal weight: 3.9990 chunk 122 optimal weight: 0.0370 chunk 88 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 221 optimal weight: 0.9980 chunk 49 optimal weight: 0.0050 chunk 232 optimal weight: 4.9990 overall best weight: 0.5874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 343 ASN G 362 ASN ** G 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 445 GLN E 350 HIS ** H 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 249 HIS K 385 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.136684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.100969 restraints weight = 45674.970| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 4.39 r_work: 0.3470 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18661 Z= 0.133 Angle : 0.757 12.035 25631 Z= 0.365 Chirality : 0.044 0.273 3068 Planarity : 0.006 0.057 3273 Dihedral : 7.203 56.153 2804 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 4.37 % Allowed : 20.46 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.16), residues: 2437 helix: -2.85 (0.35), residues: 142 sheet: -0.37 (0.18), residues: 802 loop : -2.41 (0.14), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 281 HIS 0.007 0.001 HIS F 457 PHE 0.014 0.001 PHE C 75 TYR 0.011 0.001 TYR L 411 ARG 0.011 0.001 ARG C 336 Details of bonding type rmsd link_NAG-ASN : bond 0.00447 ( 7) link_NAG-ASN : angle 2.80709 ( 21) link_BETA1-4 : bond 0.00437 ( 3) link_BETA1-4 : angle 3.69052 ( 9) hydrogen bonds : bond 0.03640 ( 450) hydrogen bonds : angle 5.19254 ( 1398) SS BOND : bond 0.00471 ( 37) SS BOND : angle 1.26161 ( 74) covalent geometry : bond 0.00310 (18614) covalent geometry : angle 0.74783 (25527) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 259 time to evaluate : 2.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 392 ARG cc_start: 0.8899 (ttp80) cc_final: 0.8574 (ttm110) REVERT: A 403 GLU cc_start: 0.9107 (pt0) cc_final: 0.8760 (pt0) REVERT: A 437 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8397 (mt-10) REVERT: B 255 ASP cc_start: 0.8927 (m-30) cc_final: 0.8722 (m-30) REVERT: B 296 ARG cc_start: 0.8324 (mmt180) cc_final: 0.8075 (tpp80) REVERT: B 385 GLN cc_start: 0.9058 (tp40) cc_final: 0.8710 (tp40) REVERT: B 423 ASP cc_start: 0.8936 (m-30) cc_final: 0.8650 (m-30) REVERT: B 428 GLU cc_start: 0.8228 (mp0) cc_final: 0.7469 (mp0) REVERT: B 464 MET cc_start: 0.7040 (ppp) cc_final: 0.6789 (ppp) REVERT: C 111 GLN cc_start: 0.7986 (pp30) cc_final: 0.7741 (pp30) REVERT: C 330 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8837 (pp20) REVERT: C 459 THR cc_start: 0.7481 (OUTLIER) cc_final: 0.6585 (t) REVERT: C 461 LYS cc_start: 0.8302 (mmtt) cc_final: 0.7902 (mmtm) REVERT: C 483 THR cc_start: 0.7412 (OUTLIER) cc_final: 0.6990 (t) REVERT: D 82 GLN cc_start: 0.9131 (mm-40) cc_final: 0.8908 (mp10) REVERT: F 340 LYS cc_start: 0.8002 (ttmt) cc_final: 0.7723 (ttmt) REVERT: F 389 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8487 (tm-30) REVERT: E 402 GLN cc_start: 0.8441 (tm-30) cc_final: 0.8220 (tm-30) REVERT: E 430 PHE cc_start: 0.7289 (m-80) cc_final: 0.6983 (m-80) REVERT: E 448 ILE cc_start: 0.6410 (OUTLIER) cc_final: 0.5944 (pp) REVERT: H 403 GLU cc_start: 0.8132 (pt0) cc_final: 0.7165 (pm20) REVERT: H 433 MET cc_start: 0.8501 (tpp) cc_final: 0.7934 (mmt) REVERT: K 338 ILE cc_start: 0.5240 (OUTLIER) cc_final: 0.5020 (mt) REVERT: K 378 ASP cc_start: 0.7625 (m-30) cc_final: 0.7271 (m-30) REVERT: K 403 GLU cc_start: 0.7528 (pt0) cc_final: 0.7093 (pt0) REVERT: K 418 ARG cc_start: 0.6233 (mtt180) cc_final: 0.5913 (mmt180) REVERT: L 367 LEU cc_start: 0.7740 (mm) cc_final: 0.7531 (mt) REVERT: L 369 CYS cc_start: 0.6642 (OUTLIER) cc_final: 0.6163 (p) REVERT: L 372 ARG cc_start: 0.6948 (ptm-80) cc_final: 0.6741 (ptm-80) REVERT: L 385 GLN cc_start: 0.6074 (OUTLIER) cc_final: 0.5132 (tp40) REVERT: L 403 GLU cc_start: 0.8812 (pt0) cc_final: 0.8426 (pm20) REVERT: L 443 PHE cc_start: 0.8048 (m-80) cc_final: 0.7105 (t80) outliers start: 82 outliers final: 38 residues processed: 314 average time/residue: 1.1391 time to fit residues: 404.0364 Evaluate side-chains 267 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 221 time to evaluate : 2.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain C residue 122 TYR Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 402 GLN Chi-restraints excluded: chain G residue 249 HIS Chi-restraints excluded: chain G residue 282 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 323 CYS Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 344 THR Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain K residue 282 THR Chi-restraints excluded: chain K residue 290 VAL Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 365 VAL Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 415 SER Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain L residue 335 THR Chi-restraints excluded: chain L residue 369 CYS Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 378 ASP Chi-restraints excluded: chain L residue 385 GLN Chi-restraints excluded: chain L residue 462 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 145 optimal weight: 0.8980 chunk 187 optimal weight: 4.9990 chunk 156 optimal weight: 4.9990 chunk 201 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 244 optimal weight: 8.9990 chunk 206 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 436 HIS H 291 GLN H 385 GLN ** K 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 385 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.131897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.096579 restraints weight = 46205.008| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 4.32 r_work: 0.3422 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 18661 Z= 0.211 Angle : 0.822 10.803 25631 Z= 0.403 Chirality : 0.046 0.280 3068 Planarity : 0.006 0.058 3273 Dihedral : 6.591 55.619 2804 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 5.86 % Allowed : 20.56 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.16), residues: 2437 helix: -2.05 (0.42), residues: 134 sheet: -0.28 (0.17), residues: 834 loop : -2.35 (0.15), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 281 HIS 0.018 0.001 HIS K 317 PHE 0.019 0.002 PHE C 75 TYR 0.014 0.002 TYR B 472 ARG 0.014 0.001 ARG C 336 Details of bonding type rmsd link_NAG-ASN : bond 0.00658 ( 7) link_NAG-ASN : angle 2.95141 ( 21) link_BETA1-4 : bond 0.00261 ( 3) link_BETA1-4 : angle 3.37431 ( 9) hydrogen bonds : bond 0.04153 ( 450) hydrogen bonds : angle 5.29694 ( 1398) SS BOND : bond 0.00532 ( 37) SS BOND : angle 1.77033 ( 74) covalent geometry : bond 0.00503 (18614) covalent geometry : angle 0.81100 (25527) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 223 time to evaluate : 2.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 GLU cc_start: 0.9249 (pt0) cc_final: 0.8809 (pt0) REVERT: A 437 GLU cc_start: 0.8932 (tt0) cc_final: 0.8658 (mt-10) REVERT: A 448 ILE cc_start: 0.9158 (tp) cc_final: 0.8957 (tt) REVERT: B 327 HIS cc_start: 0.7214 (OUTLIER) cc_final: 0.6483 (t70) REVERT: B 385 GLN cc_start: 0.9106 (OUTLIER) cc_final: 0.8812 (tp40) REVERT: B 392 ARG cc_start: 0.9150 (mmm-85) cc_final: 0.8843 (ttp-110) REVERT: B 428 GLU cc_start: 0.8451 (mp0) cc_final: 0.7979 (mp0) REVERT: C 43 ARG cc_start: 0.6793 (mmp80) cc_final: 0.6399 (tpp-160) REVERT: C 111 GLN cc_start: 0.8021 (pp30) cc_final: 0.7706 (pp30) REVERT: C 177 ILE cc_start: 0.2361 (OUTLIER) cc_final: 0.2087 (tp) REVERT: C 330 GLU cc_start: 0.9126 (OUTLIER) cc_final: 0.8867 (pt0) REVERT: C 459 THR cc_start: 0.7782 (OUTLIER) cc_final: 0.6935 (t) REVERT: F 346 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.8208 (ptt-90) REVERT: F 389 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8440 (tm-30) REVERT: G 394 LYS cc_start: 0.8777 (mmmm) cc_final: 0.8562 (mmmm) REVERT: G 451 LEU cc_start: 0.9331 (mp) cc_final: 0.9048 (pp) REVERT: E 430 PHE cc_start: 0.7297 (m-80) cc_final: 0.6914 (m-80) REVERT: E 448 ILE cc_start: 0.6708 (OUTLIER) cc_final: 0.6191 (pp) REVERT: H 315 TRP cc_start: 0.8393 (OUTLIER) cc_final: 0.7898 (t60) REVERT: H 323 CYS cc_start: 0.7075 (t) cc_final: 0.6609 (p) REVERT: H 403 GLU cc_start: 0.8238 (pt0) cc_final: 0.7356 (pm20) REVERT: H 433 MET cc_start: 0.8735 (tpp) cc_final: 0.8136 (mmm) REVERT: K 317 HIS cc_start: 0.8080 (p-80) cc_final: 0.7825 (p90) REVERT: K 338 ILE cc_start: 0.5651 (OUTLIER) cc_final: 0.5304 (mt) REVERT: K 348 GLU cc_start: 0.7439 (mp0) cc_final: 0.7211 (mp0) REVERT: K 358 GLU cc_start: 0.8301 (pt0) cc_final: 0.8063 (pt0) REVERT: K 378 ASP cc_start: 0.7897 (m-30) cc_final: 0.7536 (m-30) REVERT: K 403 GLU cc_start: 0.7491 (pt0) cc_final: 0.7086 (pt0) REVERT: K 418 ARG cc_start: 0.6639 (mtt180) cc_final: 0.6259 (mmt180) REVERT: K 433 MET cc_start: 0.8921 (mmm) cc_final: 0.8578 (mmm) REVERT: L 367 LEU cc_start: 0.8136 (mm) cc_final: 0.7840 (mt) REVERT: L 369 CYS cc_start: 0.6315 (OUTLIER) cc_final: 0.5980 (p) REVERT: L 382 ARG cc_start: 0.5768 (OUTLIER) cc_final: 0.4606 (mtm180) REVERT: L 403 GLU cc_start: 0.8987 (pt0) cc_final: 0.8594 (pm20) REVERT: L 433 MET cc_start: 0.6291 (mpm) cc_final: 0.5228 (tmt) REVERT: L 443 PHE cc_start: 0.7375 (m-80) cc_final: 0.6758 (t80) outliers start: 110 outliers final: 43 residues processed: 299 average time/residue: 1.2047 time to fit residues: 406.4597 Evaluate side-chains 254 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 200 time to evaluate : 1.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 385 GLN Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain C residue 122 TYR Chi-restraints excluded: chain C residue 160 ASP Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 402 GLN Chi-restraints excluded: chain G residue 282 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 323 CYS Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 416 ILE Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain H residue 315 TRP Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain K residue 264 LEU Chi-restraints excluded: chain K residue 290 VAL Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 365 VAL Chi-restraints excluded: chain K residue 396 LEU Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 415 SER Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain L residue 264 LEU Chi-restraints excluded: chain L residue 335 THR Chi-restraints excluded: chain L residue 369 CYS Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 382 ARG Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 462 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 70 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 205 optimal weight: 20.0000 chunk 91 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 226 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 227 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 GLN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 GLN C 11 ASN F 243 HIS F 343 ASN G 249 HIS H 385 GLN ** K 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 459 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.130773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.095946 restraints weight = 46614.369| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 4.30 r_work: 0.3389 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.4830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18661 Z= 0.192 Angle : 0.778 10.889 25631 Z= 0.379 Chirality : 0.045 0.252 3068 Planarity : 0.005 0.053 3273 Dihedral : 6.226 54.873 2804 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 5.91 % Allowed : 21.68 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.16), residues: 2437 helix: -1.48 (0.44), residues: 134 sheet: -0.17 (0.18), residues: 804 loop : -2.24 (0.15), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 281 HIS 0.011 0.001 HIS H 327 PHE 0.017 0.002 PHE C 75 TYR 0.014 0.001 TYR C 148 ARG 0.016 0.001 ARG C 336 Details of bonding type rmsd link_NAG-ASN : bond 0.00573 ( 7) link_NAG-ASN : angle 2.99113 ( 21) link_BETA1-4 : bond 0.00287 ( 3) link_BETA1-4 : angle 2.84631 ( 9) hydrogen bonds : bond 0.03691 ( 450) hydrogen bonds : angle 5.10118 ( 1398) SS BOND : bond 0.00792 ( 37) SS BOND : angle 1.62721 ( 74) covalent geometry : bond 0.00458 (18614) covalent geometry : angle 0.76846 (25527) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 232 time to evaluate : 2.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 GLU cc_start: 0.9186 (pt0) cc_final: 0.8780 (pt0) REVERT: A 437 GLU cc_start: 0.8954 (tt0) cc_final: 0.8691 (mt-10) REVERT: A 457 HIS cc_start: 0.7670 (OUTLIER) cc_final: 0.7312 (p90) REVERT: B 385 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.8785 (tp40) REVERT: B 403 GLU cc_start: 0.8716 (pt0) cc_final: 0.8250 (pm20) REVERT: B 428 GLU cc_start: 0.8516 (mp0) cc_final: 0.8013 (mp0) REVERT: B 464 MET cc_start: 0.7152 (ppp) cc_final: 0.6808 (ppp) REVERT: C 43 ARG cc_start: 0.7080 (mmp80) cc_final: 0.6671 (mmp80) REVERT: C 111 GLN cc_start: 0.8017 (pp30) cc_final: 0.7699 (pp30) REVERT: C 177 ILE cc_start: 0.2838 (OUTLIER) cc_final: 0.2306 (tp) REVERT: C 330 GLU cc_start: 0.9112 (OUTLIER) cc_final: 0.8862 (pt0) REVERT: C 424 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6658 (pp) REVERT: F 346 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8185 (ptt-90) REVERT: F 389 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8475 (tm-30) REVERT: F 403 GLU cc_start: 0.9114 (pt0) cc_final: 0.8788 (pt0) REVERT: G 348 GLU cc_start: 0.8338 (mp0) cc_final: 0.7945 (mp0) REVERT: G 394 LYS cc_start: 0.8859 (mmmm) cc_final: 0.8537 (mmtp) REVERT: G 470 THR cc_start: 0.8898 (m) cc_final: 0.8677 (p) REVERT: E 352 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8403 (mm) REVERT: E 445 GLN cc_start: 0.6825 (OUTLIER) cc_final: 0.6512 (tm-30) REVERT: E 448 ILE cc_start: 0.6640 (OUTLIER) cc_final: 0.5895 (mp) REVERT: H 315 TRP cc_start: 0.8452 (OUTLIER) cc_final: 0.7933 (t60) REVERT: H 403 GLU cc_start: 0.8366 (pt0) cc_final: 0.7522 (pm20) REVERT: H 433 MET cc_start: 0.8727 (tpp) cc_final: 0.8260 (mmm) REVERT: K 338 ILE cc_start: 0.5812 (OUTLIER) cc_final: 0.5464 (mt) REVERT: K 348 GLU cc_start: 0.7509 (mp0) cc_final: 0.6952 (mp0) REVERT: K 358 GLU cc_start: 0.8292 (pt0) cc_final: 0.7890 (pt0) REVERT: K 378 ASP cc_start: 0.8008 (m-30) cc_final: 0.7720 (m-30) REVERT: K 403 GLU cc_start: 0.7465 (pt0) cc_final: 0.7099 (pt0) REVERT: K 418 ARG cc_start: 0.6923 (mtt180) cc_final: 0.6554 (mmt180) REVERT: K 433 MET cc_start: 0.8844 (mmm) cc_final: 0.8209 (mmm) REVERT: L 367 LEU cc_start: 0.8395 (mm) cc_final: 0.8155 (mt) REVERT: L 401 ARG cc_start: 0.7394 (mmt-90) cc_final: 0.7169 (mmt180) REVERT: L 403 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8472 (pm20) REVERT: L 433 MET cc_start: 0.6240 (mpm) cc_final: 0.5789 (mtp) outliers start: 111 outliers final: 41 residues processed: 308 average time/residue: 1.1418 time to fit residues: 397.7514 Evaluate side-chains 258 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 205 time to evaluate : 2.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 457 HIS Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 385 GLN Chi-restraints excluded: chain C residue 122 TYR Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 402 GLN Chi-restraints excluded: chain G residue 249 HIS Chi-restraints excluded: chain G residue 282 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 323 CYS Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 416 ILE Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 368 THR Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 445 GLN Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain H residue 315 TRP Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 375 SER Chi-restraints excluded: chain K residue 290 VAL Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 359 LEU Chi-restraints excluded: chain K residue 365 VAL Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain L residue 284 SER Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 378 ASP Chi-restraints excluded: chain L residue 381 VAL Chi-restraints excluded: chain L residue 403 GLU Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 462 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 10 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 192 optimal weight: 0.5980 chunk 150 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 1 optimal weight: 0.0050 chunk 22 optimal weight: 0.1980 chunk 147 optimal weight: 0.9980 chunk 218 optimal weight: 6.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 343 ASN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 249 HIS H 291 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.132077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.097364 restraints weight = 46512.721| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 4.35 r_work: 0.3427 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.5047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18661 Z= 0.132 Angle : 0.751 11.383 25631 Z= 0.362 Chirality : 0.044 0.247 3068 Planarity : 0.005 0.078 3273 Dihedral : 5.894 55.063 2804 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 3.73 % Allowed : 25.04 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.17), residues: 2437 helix: -1.11 (0.49), residues: 122 sheet: -0.01 (0.18), residues: 822 loop : -2.14 (0.15), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 281 HIS 0.011 0.001 HIS H 327 PHE 0.014 0.001 PHE E 430 TYR 0.012 0.001 TYR C 148 ARG 0.016 0.001 ARG C 336 Details of bonding type rmsd link_NAG-ASN : bond 0.00478 ( 7) link_NAG-ASN : angle 2.67411 ( 21) link_BETA1-4 : bond 0.00315 ( 3) link_BETA1-4 : angle 2.57943 ( 9) hydrogen bonds : bond 0.03191 ( 450) hydrogen bonds : angle 4.86367 ( 1398) SS BOND : bond 0.00384 ( 37) SS BOND : angle 1.32530 ( 74) covalent geometry : bond 0.00319 (18614) covalent geometry : angle 0.74349 (25527) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 223 time to evaluate : 2.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 GLU cc_start: 0.9161 (pt0) cc_final: 0.8756 (pt0) REVERT: A 437 GLU cc_start: 0.8952 (tt0) cc_final: 0.8730 (mt-10) REVERT: A 457 HIS cc_start: 0.7596 (OUTLIER) cc_final: 0.7304 (p90) REVERT: A 464 MET cc_start: 0.9115 (mmm) cc_final: 0.8860 (mmm) REVERT: B 327 HIS cc_start: 0.7369 (OUTLIER) cc_final: 0.6540 (t70) REVERT: B 385 GLN cc_start: 0.9082 (tp40) cc_final: 0.8775 (tp40) REVERT: B 392 ARG cc_start: 0.9111 (mmm-85) cc_final: 0.8731 (ttp-110) REVERT: B 403 GLU cc_start: 0.8693 (pt0) cc_final: 0.8245 (pm20) REVERT: B 428 GLU cc_start: 0.8511 (mp0) cc_final: 0.8029 (mp0) REVERT: B 464 MET cc_start: 0.7259 (ppp) cc_final: 0.6945 (ppp) REVERT: C 43 ARG cc_start: 0.6977 (mmp80) cc_final: 0.6768 (mmp80) REVERT: C 111 GLN cc_start: 0.8081 (pp30) cc_final: 0.7733 (pp30) REVERT: C 177 ILE cc_start: 0.3847 (OUTLIER) cc_final: 0.3413 (tp) REVERT: C 217 LEU cc_start: 0.5862 (OUTLIER) cc_final: 0.5602 (tp) REVERT: C 330 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8875 (pt0) REVERT: C 424 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6852 (pp) REVERT: F 346 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.8115 (ptt-90) REVERT: F 389 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8388 (tm-30) REVERT: G 348 GLU cc_start: 0.8331 (mp0) cc_final: 0.7960 (mp0) REVERT: G 393 GLU cc_start: 0.8892 (pm20) cc_final: 0.8669 (pm20) REVERT: G 394 LYS cc_start: 0.8864 (mmmm) cc_final: 0.8540 (mmmt) REVERT: E 258 LEU cc_start: 0.6746 (mm) cc_final: 0.6230 (tp) REVERT: E 445 GLN cc_start: 0.6952 (OUTLIER) cc_final: 0.6692 (tm-30) REVERT: E 448 ILE cc_start: 0.6688 (OUTLIER) cc_final: 0.5969 (mp) REVERT: H 315 TRP cc_start: 0.8457 (OUTLIER) cc_final: 0.8000 (t60) REVERT: H 385 GLN cc_start: 0.9428 (tt0) cc_final: 0.9103 (tp-100) REVERT: H 403 GLU cc_start: 0.8394 (pt0) cc_final: 0.7636 (pm20) REVERT: H 433 MET cc_start: 0.8619 (tpp) cc_final: 0.8118 (mmm) REVERT: K 317 HIS cc_start: 0.7899 (p90) cc_final: 0.7698 (p-80) REVERT: K 338 ILE cc_start: 0.5835 (OUTLIER) cc_final: 0.5489 (mt) REVERT: K 358 GLU cc_start: 0.8317 (pt0) cc_final: 0.7932 (pt0) REVERT: K 378 ASP cc_start: 0.7994 (m-30) cc_final: 0.7681 (m-30) REVERT: K 403 GLU cc_start: 0.7435 (pt0) cc_final: 0.7095 (pt0) REVERT: K 418 ARG cc_start: 0.6958 (mtt180) cc_final: 0.6601 (mmt180) REVERT: K 433 MET cc_start: 0.8854 (mmm) cc_final: 0.8244 (mmm) REVERT: L 367 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8284 (mt) REVERT: L 401 ARG cc_start: 0.7411 (mmt-90) cc_final: 0.7174 (mmt180) REVERT: L 403 GLU cc_start: 0.8848 (pt0) cc_final: 0.8428 (pm20) REVERT: L 433 MET cc_start: 0.6437 (mpm) cc_final: 0.6170 (mmt) outliers start: 70 outliers final: 43 residues processed: 269 average time/residue: 1.2169 time to fit residues: 367.1356 Evaluate side-chains 263 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 208 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 457 HIS Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain C residue 122 TYR Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain G residue 282 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 368 THR Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 445 GLN Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain H residue 315 TRP Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 375 SER Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 365 VAL Chi-restraints excluded: chain K residue 396 LEU Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain L residue 284 SER Chi-restraints excluded: chain L residue 367 LEU Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 462 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.4128 > 50: distance: 8 - 13: 7.301 distance: 13 - 14: 5.724 distance: 14 - 15: 7.543 distance: 14 - 17: 3.722 distance: 15 - 16: 7.217 distance: 15 - 27: 14.733 distance: 17 - 18: 10.768 distance: 18 - 19: 4.507 distance: 18 - 20: 20.022 distance: 19 - 21: 19.576 distance: 20 - 22: 17.232 distance: 20 - 23: 13.485 distance: 21 - 22: 17.625 distance: 22 - 24: 16.198 distance: 23 - 25: 5.689 distance: 24 - 26: 4.842 distance: 25 - 26: 5.271 distance: 27 - 28: 20.794 distance: 28 - 29: 11.760 distance: 28 - 31: 6.956 distance: 29 - 30: 20.214 distance: 29 - 34: 28.021 distance: 31 - 32: 16.531 distance: 31 - 33: 19.010 distance: 34 - 35: 34.314 distance: 34 - 40: 21.768 distance: 35 - 36: 16.292 distance: 35 - 38: 14.460 distance: 36 - 37: 11.043 distance: 36 - 41: 18.737 distance: 38 - 39: 12.745 distance: 39 - 40: 10.709 distance: 41 - 42: 16.353 distance: 42 - 43: 7.386 distance: 42 - 45: 4.559 distance: 43 - 44: 16.191 distance: 43 - 47: 9.404 distance: 45 - 46: 7.399 distance: 47 - 48: 4.713 distance: 48 - 49: 5.210 distance: 48 - 51: 4.896 distance: 49 - 50: 8.866 distance: 49 - 53: 6.072 distance: 51 - 52: 5.776 distance: 53 - 54: 10.236 distance: 54 - 55: 8.417 distance: 55 - 56: 17.158 distance: 55 - 57: 5.303 distance: 57 - 58: 12.618 distance: 58 - 59: 10.075 distance: 58 - 61: 16.193 distance: 59 - 60: 8.462 distance: 59 - 62: 13.236 distance: 62 - 63: 6.947 distance: 63 - 64: 19.268 distance: 63 - 66: 19.262 distance: 64 - 65: 15.844 distance: 64 - 68: 18.276 distance: 66 - 67: 30.562 distance: 68 - 69: 17.036 distance: 69 - 70: 14.752 distance: 69 - 72: 13.712 distance: 70 - 71: 26.492 distance: 70 - 73: 19.180 distance: 73 - 74: 30.983 distance: 74 - 75: 23.250 distance: 74 - 77: 14.816 distance: 75 - 76: 19.042 distance: 75 - 80: 17.180 distance: 77 - 78: 30.608 distance: 77 - 79: 23.997